I: pbuilder: network access will be disabled during build I: Current time: Sun Apr 12 14:37:08 +14 2026 I: pbuilder-time-stamp: 1775954228 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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: Copying source file I: copying [rdkit_202409.6-2.dsc] I: copying [./rdkit_202409.6.orig.tar.xz] I: copying [./rdkit_202409.6-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./rdkit_202409.6-2.dsc: unsupported subcommand dpkg-source: info: extracting rdkit in rdkit-202409.6 dpkg-source: info: unpacking rdkit_202409.6.orig.tar.xz dpkg-source: info: unpacking rdkit_202409.6-2.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 postgres_cmakelists_fixes.patch dpkg-source: info: applying disable_pgsql_test.patch dpkg-source: info: applying fix_inchi_linking.patch dpkg-source: info: applying disable_inchi_test.patch dpkg-source: info: applying disable_python_test.patch dpkg-source: info: applying disable_riscv64_timeout_tests.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2068256/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Apr 12 00:37 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2068256/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2068256/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=23f6d0e8df474f4993cdeda5b5b40615 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2068256 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.PfaUNweg/pbuilderrc_B6tE --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.PfaUNweg/b2 --logfile b2/build.log rdkit_202409.6-2.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2068256/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: arm64 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: architecture-is-64-bit, architecture-is-little-endian, bison, catch2, cmake, debhelper-compat (= 13), dh-python, doxygen, flex, imagemagick, latexmk, libboost-dev, libboost-iostreams-dev, libboost-numpy-dev, libboost-program-options-dev, libboost-python-dev, libboost-regex-dev, libboost-system-dev, libboost-thread-dev, libcairo2-dev, libcoordgen-dev, libeigen3-dev, libfreetype-dev, libinchi-dev (>= 1.07.1+dfsg-2), 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-pytest, 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 ... 19897 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 architecture-is-64-bit; however: Package architecture-is-64-bit is not installed. pbuilder-satisfydepends-dummy depends on architecture-is-little-endian; however: Package architecture-is-little-endian is not installed. 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-numpy-dev; however: Package libboost-numpy-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-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 libinchi-dev (>= 1.07.1+dfsg-2); however: Package libinchi-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-pytest; however: Package python3-pytest 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: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bison{a} bsdextrautils{a} ca-certificates{a} catch2{a} clang-19{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} girepository-tools{a} groff-base{a} hicolor-icon-theme{a} icu-devtools{a} imagemagick{a} imagemagick-7-common{a} imagemagick-7.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-numpy-dev{a} libboost-numpy1.83-dev{a} libboost-numpy1.83.0{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{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} libbz2-dev{a} libcairo-gobject2{a} libcairo-script-interpreter2{a} libcairo2{a} libcairo2-dev{a} libcatch2-dev{a} libclang-common-19-dev{a} libclang-cpp19{a} libclang1-19{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} libffi8{a} libfftw3-double3{a} libfile-stripnondeterminism-perl{a} libfmt10{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} libgio-2.0-dev{a} libgio-2.0-dev-bin{a} libgirepository-2.0-0{a} libglib2.0-0t64{a} libglib2.0-bin{a} libglib2.0-data{a} libglib2.0-dev{a} libglib2.0-dev-bin{a} libgnutls30t64{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} libidn2-0{a} libimagequant0{a} libinchi-dev{a} libinchi1.07{a} libio-pty-perl{a} libipc-run-perl{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} libllvm19{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-7.q16-10{a} libmagickwand-7.q16-10{a} libmount-dev{a} libmpfi0{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libnuma1{a} libobjc-14-dev{a} libobjc4{a} libopenjp2-7{a} libp11-kit0{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{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} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} libraw23t64{a} libreadline8t64{a} librhash1{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} libsynctex2{a} libsysprof-capture-4-dev{a} libtasn1-6{a} libteckit0{a} libtexlua53-5{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{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-19{a} llvm-19-dev{a} llvm-19-linker-tools{a} llvm-19-runtime{a} llvm-19-tools{a} m4{a} man-db{a} media-types{a} native-architecture{a} netbase{a} openssl{a} pandoc{a} pandoc-data{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} postgresql-client-17{a} postgresql-client-common{a} postgresql-common{a} postgresql-common-dev{a} postgresql-server-dev-17{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-defusedxml{a} python3-dev{a} python3-docutils{a} python3-greenlet{a} python3-idna{a} python3-imagesize{a} python3-iniconfig{a} python3-jinja2{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-numpy-dev{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pluggy{a} python3-pygments{a} python3-pytest{a} python3-pytz{a} python3-recommonmark{a} python3-requests{a} python3-roman{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sqlalchemy{a} python3-typing-extensions{a} python3-tz{a} python3-urllib3{a} python3-yaml{a} python3.13{a} python3.13-dev{a} python3.13-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-19-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-7.q16-10-extra libmail-sendmail-perl libnet-dbus-perl libpng-tools librsvg2-common libsasl2-modules libspreadsheet-parseexcel-perl libx11-protocol-perl linux-sysctl-defaults lmodern logrotate lynx mupdf netpbm okular papers 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, 369 newly installed, 0 to remove and 0 not upgraded. Need to get 396 MB of archives. After unpacking 2113 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-7 [285 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 flex arm64 2.6.4-8.2+b4 [412 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libfftw3-double3 arm64 3.3.10-2+b1 [337 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.47-1 [274 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-2.1 [318 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-2.1 [387 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libdav1d7 arm64 1.5.1-1 [252 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-dav1d arm64 1.19.5-1+b1 [11.5 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libde265-0 arm64 1.0.15-1+b3 [153 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-libde265 arm64 1.19.5-1+b1 [15.4 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libheif1 arm64 1.19.5-1+b1 [438 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3.1 [173 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.7-1 [21.2 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.83.5-1 [1422 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 liblqr-1-0 arm64 0.4.2-2.1+b2 [27.0 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.5.4-4 [415 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.3-1 [189 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libraw23t64 arm64 0.21.3-1+b1 [370 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [113 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.5.0-0.1 [125 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [630 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 imagemagick-7-common all 8:7.1.1.43+dfsg1-1 [67.4 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libmagickcore-7.q16-10 arm64 8:7.1.1.43+dfsg1-1 [1647 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libmagickwand-7.q16-10 arm64 8:7.1.1.43+dfsg1-1 [268 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 postgresql-client-common all 274 [46.5 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libio-pty-perl arm64 1:1.20-1+b2 [34.0 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 postgresql-common-dev all 274 [71.8 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.4.1-1 [1390 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 ssl-cert all 1.1.3 [16.8 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B] Get: 53 http://deb.debian.org/debian unstable/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 54 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-7 [62.4 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-7 [868 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0050 [42.7 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 postgresql-common all 274 [111 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.2-1 [853 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.2-1 [1997 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.2-2 [27.1 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 media-types all 13.0.0 [29.3 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025a-2 [259 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.2-1 [1914 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.2-1 [745 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.2-2 [10.1 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.2-2 [28.1 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-4 [136 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.1-2 [104 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-17 [361 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:2.2.3+ds-4 [3596 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20241223 [164 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 architecture-properties arm64 0.2.6 [2336 B] Get: 87 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-3 [862 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 bison arm64 2:3.8.2+dfsg-1+b2 [1149 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libcatch2-dev arm64 3.7.1-0.5 [588 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 catch2 all 3.7.1-0.5 [5144 B] Get: 94 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libllvm19 arm64 1:19.1.7-1+b1 [23.3 MB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libclang-cpp19 arm64 1:19.1.7-1+b1 [12.0 MB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libgc1 arm64 1:8.2.8-1 [241 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libobjc4 arm64 14.2.0-17 [39.3 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libobjc-14-dev arm64 14.2.0-17 [166 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libclang-common-19-dev arm64 1:19.1.7-1+b1 [740 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 llvm-19-linker-tools arm64 1:19.1.7-1+b1 [1100 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libclang1-19 arm64 1:19.1.7-1+b1 [6851 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 clang-19 arm64 1:19.1.7-1+b1 [112 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.6-1 [2268 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-4 [32.2 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 111 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-4 [308 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.8.0-1 [63.2 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.12.1-3 [339 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.50.0-2 [148 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.6-1 [9912 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 137 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250308 [115 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libfmt10 arm64 10.1.1+ds1-4 [121 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 doxygen arm64 1.9.8+ds-2.1 [4519 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-2.1 [463 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 fonts-lmodern all 2.005-1 [4540 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 native-architecture all 0.2.6 [2264 B] Get: 151 http://deb.debian.org/debian unstable/main arm64 libgirepository-2.0-0 arm64 2.83.5-1 [132 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 girepository-tools arm64 2.83.5-1 [137 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 hicolor-icon-theme all 0.18-2 [11.8 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 icu-devtools arm64 72.1-6 [196 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 imagemagick-7.q16 arm64 8:7.1.1.43+dfsg1-1 [726 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 imagemagick arm64 8:7.1.1.43+dfsg1-1 [20.0 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 tex-common all 6.19 [29.4 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 libpaper2 arm64 2.2.5-0.3+b1 [16.6 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 2.2.5-0.3+b1 [16.3 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 libkpathsea6 arm64 2024.20240313.70630+ds-5+b1 [154 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 libptexenc1 arm64 2024.20240313.70630+ds-5+b1 [48.2 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 libsynctex2 arm64 2024.20240313.70630+ds-5+b1 [60.6 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-5+b1 [106 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 t1utils arm64 1.41-4+b1 [57.6 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b4 [27.2 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.2.0-1 [443 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 libmpfi0 arm64 1.5.4+ds-4 [34.5 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 libpotrace0 arm64 1.16-2+b2 [23.4 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 libteckit0 arm64 2.5.12+ds1-1+b1 [303 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+24 [217 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b2 [173 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 libxmu6 arm64 2:1.1.3-3+b4 [55.7 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 libxpm4 arm64 1:3.5.17-1+b3 [53.4 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 libxaw7 arm64 2:1.0.16-1 [195 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 libzzip-0-13t64 arm64 0.13.78+dfsg.1-0.1 [59.4 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 texlive-binaries arm64 2024.20240313.70630+ds-5+b1 [7357 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 texlive-base all 2024.20250114-1 [22.8 MB] Get: 187 http://deb.debian.org/debian unstable/main arm64 texlive-latex-base all 2024.20250114-1 [1282 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 latexmk all 1:4.86~ds-1 [507 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 libapache-pom-java all 33-2 [5852 B] Get: 190 http://deb.debian.org/debian unstable/main arm64 uuid-dev arm64 2.40.4-5 [48.5 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 libblkid-dev arm64 2.40.4-5 [209 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-4.1+b1 [10.6 MB] Get: 193 http://deb.debian.org/debian unstable/main arm64 libboost-atomic1.83.0 arm64 1.83.0-4.1+b1 [234 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 libboost-atomic1.83-dev arm64 1.83.0-4.1+b1 [235 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 libboost-chrono1.83.0t64 arm64 1.83.0-4.1+b1 [240 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 libboost-chrono1.83-dev arm64 1.83.0-4.1+b1 [245 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 libboost-date-time1.83.0 arm64 1.83.0-4.1+b1 [231 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 libboost-serialization1.83.0 arm64 1.83.0-4.1+b1 [325 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 libboost-serialization1.83-dev arm64 1.83.0-4.1+b1 [373 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 libboost-date-time1.83-dev arm64 1.83.0-4.1+b1 [239 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 202 http://deb.debian.org/debian unstable/main arm64 libboost-regex1.83.0 arm64 1.83.0-4.1+b1 [315 kB] Get: 203 http://deb.debian.org/debian unstable/main arm64 libicu-dev arm64 72.1-6 [10.3 MB] Get: 204 http://deb.debian.org/debian unstable/main arm64 libboost-regex1.83-dev arm64 1.83.0-4.1+b1 [335 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 libboost-iostreams1.83-dev arm64 1.83.0-4.1+b1 [261 kB] Get: 206 http://deb.debian.org/debian unstable/main arm64 libboost-iostreams-dev arm64 1.83.0.2+b2 [3568 B] Get: 207 http://deb.debian.org/debian unstable/main arm64 libboost-python1.83.0 arm64 1.83.0-4.1+b1 [297 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 libboost-numpy1.83.0 arm64 1.83.0-4.1+b1 [241 kB] Get: 209 http://deb.debian.org/debian unstable/main arm64 libboost-numpy1.83-dev arm64 1.83.0-4.1+b1 [246 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 libboost-numpy-dev arm64 1.83.0.2+b2 [3632 B] Get: 211 http://deb.debian.org/debian unstable/main arm64 libboost-program-options1.83.0 arm64 1.83.0-4.1+b1 [331 kB] Get: 212 http://deb.debian.org/debian unstable/main arm64 libboost-program-options1.83-dev arm64 1.83.0-4.1+b1 [369 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 libboost-program-options-dev arm64 1.83.0.2+b2 [3600 B] Get: 214 http://deb.debian.org/debian unstable/main arm64 libpython3.13 arm64 3.13.2-1 [1970 kB] Get: 215 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB] Get: 216 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 libpython3.13-dev arm64 3.13.2-1 [4678 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.13.2-2 [10.3 kB] Get: 219 http://deb.debian.org/debian unstable/main arm64 python3.13-dev arm64 3.13.2-1 [505 kB] Get: 220 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 221 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 222 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 223 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.13.2-2 [26.1 kB] Get: 224 http://deb.debian.org/debian unstable/main arm64 libboost-python1.83-dev arm64 1.83.0-4.1+b1 [322 kB] Get: 225 http://deb.debian.org/debian unstable/main arm64 libboost-python-dev arm64 1.83.0.2+b2 [3880 B] Get: 226 http://deb.debian.org/debian unstable/main arm64 libboost-regex-dev arm64 1.83.0.2+b2 [3852 B] Get: 227 http://deb.debian.org/debian unstable/main arm64 libboost-system1.83.0 arm64 1.83.0-4.1+b1 [231 kB] Get: 228 http://deb.debian.org/debian unstable/main arm64 libboost-system1.83-dev arm64 1.83.0-4.1+b1 [232 kB] Get: 229 http://deb.debian.org/debian unstable/main arm64 libboost-system-dev arm64 1.83.0.2+b2 [3720 B] Get: 230 http://deb.debian.org/debian unstable/main arm64 libboost-thread1.83.0 arm64 1.83.0-4.1+b1 [266 kB] Get: 231 http://deb.debian.org/debian unstable/main arm64 libboost-thread1.83-dev arm64 1.83.0-4.1+b1 [277 kB] Get: 232 http://deb.debian.org/debian unstable/main arm64 libboost-thread-dev arm64 1.83.0.2+b2 [3616 B] Get: 233 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b7 [308 kB] Get: 234 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 235 http://deb.debian.org/debian unstable/main arm64 libcairo-gobject2 arm64 1.18.2-2 [130 kB] Get: 236 http://deb.debian.org/debian unstable/main arm64 liblzo2-2 arm64 2.10-3+b1 [49.6 kB] Get: 237 http://deb.debian.org/debian unstable/main arm64 libcairo-script-interpreter2 arm64 1.18.2-2 [57.4 kB] Get: 238 http://deb.debian.org/debian unstable/main arm64 libpng-dev arm64 1.6.47-1 [360 kB] Get: 239 http://deb.debian.org/debian unstable/main arm64 libfreetype-dev arm64 2.13.3+dfsg-1 [600 kB] Get: 240 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 241 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 242 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 243 http://deb.debian.org/debian unstable/main arm64 libfontconfig-dev arm64 2.15.0-2.1 [412 kB] Get: 244 http://deb.debian.org/debian unstable/main arm64 libffi-dev arm64 3.4.7-1 [57.1 kB] Get: 245 http://deb.debian.org/debian unstable/main arm64 libsepol-dev arm64 3.8-1 [356 kB] Get: 246 http://deb.debian.org/debian unstable/main arm64 libpcre2-16-0 arm64 10.45-1 [247 kB] Get: 247 http://deb.debian.org/debian unstable/main arm64 libpcre2-32-0 arm64 10.45-1 [237 kB] Get: 248 http://deb.debian.org/debian unstable/main arm64 libpcre2-posix3 arm64 10.45-1 [63.7 kB] Get: 249 http://deb.debian.org/debian unstable/main arm64 libpcre2-dev arm64 10.45-1 [749 kB] Get: 250 http://deb.debian.org/debian unstable/main arm64 libselinux1-dev arm64 3.8-4 [172 kB] Get: 251 http://deb.debian.org/debian unstable/main arm64 libmount-dev arm64 2.40.4-5 [29.6 kB] Get: 252 http://deb.debian.org/debian unstable/main arm64 libsysprof-capture-4-dev arm64 48~beta-2 [49.5 kB] Get: 253 http://deb.debian.org/debian unstable/main arm64 libgio-2.0-dev arm64 2.83.5-1 [1706 kB] Get: 254 http://deb.debian.org/debian unstable/main arm64 libglib2.0-data all 2.83.5-1 [1284 kB] Get: 255 http://deb.debian.org/debian unstable/main arm64 libglib2.0-bin arm64 2.83.5-1 [124 kB] Get: 256 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 257 http://deb.debian.org/debian unstable/main arm64 libgio-2.0-dev-bin arm64 2.83.5-1 [163 kB] Get: 258 http://deb.debian.org/debian unstable/main arm64 libglib2.0-dev-bin arm64 2.83.5-1 [52.7 kB] Get: 259 http://deb.debian.org/debian unstable/main arm64 libglib2.0-dev arm64 2.83.5-1 [53.5 kB] Get: 260 http://deb.debian.org/debian unstable/main arm64 libpixman-1-dev arm64 0.44.0-3 [11.4 kB] Get: 261 http://deb.debian.org/debian unstable/main arm64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 262 http://deb.debian.org/debian unstable/main arm64 x11proto-dev all 2024.1-1 [603 kB] Get: 263 http://deb.debian.org/debian unstable/main arm64 x11proto-core-dev all 2024.1-1 [3312 B] Get: 264 http://deb.debian.org/debian unstable/main arm64 libice-dev arm64 2:1.1.1-1 [73.0 kB] Get: 265 http://deb.debian.org/debian unstable/main arm64 libsm-dev arm64 2:1.2.4-1 [38.0 kB] Get: 266 http://deb.debian.org/debian unstable/main arm64 libxau-dev arm64 1:1.0.11-1 [23.9 kB] Get: 267 http://deb.debian.org/debian unstable/main arm64 libxdmcp-dev arm64 1:1.1.5-1 [44.2 kB] Get: 268 http://deb.debian.org/debian unstable/main arm64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 269 http://deb.debian.org/debian unstable/main arm64 libxcb1-dev arm64 1.17.0-2+b1 [182 kB] Get: 270 http://deb.debian.org/debian unstable/main arm64 libx11-dev arm64 2:1.8.10-2 [877 kB] Get: 271 http://deb.debian.org/debian unstable/main arm64 libxcb-render0-dev arm64 1.17.0-2+b1 [119 kB] Get: 272 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0-dev arm64 1.17.0-2+b1 [108 kB] Get: 273 http://deb.debian.org/debian unstable/main arm64 libxext-dev arm64 2:1.3.4-1+b3 [105 kB] Get: 274 http://deb.debian.org/debian unstable/main arm64 libxrender-dev arm64 1:0.9.10-1.1+b4 [35.7 kB] Get: 275 http://deb.debian.org/debian unstable/main arm64 libcairo2-dev arm64 1.18.2-2 [43.0 kB] Get: 276 http://deb.debian.org/debian unstable/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 277 http://deb.debian.org/debian unstable/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 278 http://deb.debian.org/debian unstable/main arm64 libcoordgen3 arm64 3.0.2-1+b2 [204 kB] Get: 279 http://deb.debian.org/debian unstable/main arm64 libcoordgen-dev arm64 3.0.2-1+b2 [46.9 kB] Get: 280 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 281 http://deb.debian.org/debian unstable/main arm64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 282 http://deb.debian.org/debian unstable/main arm64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 283 http://deb.debian.org/debian unstable/main arm64 libfontenc1 arm64 1:1.1.8-1+b2 [22.5 kB] Get: 284 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 285 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB] Get: 286 http://deb.debian.org/debian unstable/main arm64 shared-mime-info arm64 2.4-5+b2 [756 kB] Get: 287 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-2 [131 kB] Get: 288 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 289 http://deb.debian.org/debian unstable/main arm64 libinchi1.07 arm64 1.07.3+dfsg-1 [499 kB] Get: 290 http://deb.debian.org/debian unstable/main arm64 libinchi-dev arm64 1.07.3+dfsg-1 [19.6 kB] Get: 291 http://deb.debian.org/debian unstable/main arm64 liblua5.4-0 arm64 5.4.7-1+b2 [134 kB] Get: 292 http://deb.debian.org/debian unstable/main arm64 libmaeparser1 arm64 1.3.1-1+b2 [84.6 kB] Get: 293 http://deb.debian.org/debian unstable/main arm64 libmaeparser-dev arm64 1.3.1-1+b2 [13.6 kB] Get: 294 http://deb.debian.org/debian unstable/main arm64 libncurses6 arm64 6.5+20250216-2 [96.1 kB] Get: 295 http://deb.debian.org/debian unstable/main arm64 libncurses-dev arm64 6.5+20250216-2 [340 kB] Get: 296 http://deb.debian.org/debian unstable/main arm64 libnuma1 arm64 2.0.18-1+b1 [21.8 kB] Get: 297 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 298 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 299 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.56.1-1 [213 kB] Get: 300 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.56.1-1 [52.8 kB] Get: 301 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.56.1-1 [33.8 kB] Get: 302 http://deb.debian.org/debian unstable/main arm64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 303 http://deb.debian.org/debian unstable/main arm64 libpfm4 arm64 4.13.0+git83-g91970fe-1 [63.6 kB] Get: 304 http://deb.debian.org/debian unstable/main arm64 libpq5 arm64 17.4-1 [219 kB] Get: 305 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.4.1-1 [3232 kB] Get: 306 http://deb.debian.org/debian unstable/main arm64 libpq-dev arm64 17.4-1 [146 kB] Get: 307 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.2-1 [13.6 kB] Get: 308 http://deb.debian.org/debian unstable/main arm64 librsvg2-2 arm64 2.59.90+dfsg-2 [1573 kB] Get: 309 http://deb.debian.org/debian unstable/main arm64 librsvg2-bin arm64 2.59.90+dfsg-2 [1723 kB] Get: 310 http://deb.debian.org/debian unstable/main arm64 libsqlite3-dev arm64 3.46.1-2 [1058 kB] Get: 311 http://deb.debian.org/debian unstable/main arm64 libxml2-dev arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [751 kB] Get: 312 http://deb.debian.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-2 [49.2 kB] Get: 313 http://deb.debian.org/debian unstable/main arm64 libz3-dev arm64 4.13.3-1 [107 kB] Get: 314 http://deb.debian.org/debian unstable/main arm64 llvm-19-runtime arm64 1:19.1.7-1+b1 [504 kB] Get: 315 http://deb.debian.org/debian unstable/main arm64 llvm-19 arm64 1:19.1.7-1+b1 [14.7 MB] Get: 316 http://deb.debian.org/debian unstable/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 317 http://deb.debian.org/debian unstable/main arm64 python3-yaml arm64 6.0.2-1+b2 [122 kB] Get: 318 http://deb.debian.org/debian unstable/main arm64 llvm-19-tools arm64 1:19.1.7-1+b1 [489 kB] Get: 319 http://deb.debian.org/debian unstable/main arm64 llvm-19-dev arm64 1:19.1.7-1+b1 [40.1 MB] Get: 320 http://deb.debian.org/debian unstable/main arm64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 321 http://deb.debian.org/debian unstable/main arm64 pandoc arm64 3.1.11.1+ds-2 [26.2 MB] Get: 322 http://deb.debian.org/debian unstable/main arm64 postgresql-client-17 arm64 17.4-1 [1985 kB] Get: 323 http://deb.debian.org/debian unstable/main arm64 postgresql-server-dev-17 arm64 17.4-1 [1308 kB] Get: 324 http://deb.debian.org/debian unstable/main arm64 postgresql-server-dev-all all 274 [13.5 kB] Get: 325 http://deb.debian.org/debian unstable/main arm64 preview-latex-style all 13.2-1 [350 kB] Get: 326 http://deb.debian.org/debian unstable/main arm64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 327 http://deb.debian.org/debian unstable/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 328 http://deb.debian.org/debian unstable/main arm64 python3-babel all 2.17.0-1 [117 kB] Get: 329 http://deb.debian.org/debian unstable/main arm64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 330 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 331 http://deb.debian.org/debian unstable/main arm64 python3-charset-normalizer arm64 3.4.1-1+b1 [119 kB] Get: 332 http://deb.debian.org/debian unstable/main arm64 python3-commonmark all 0.9.1-8 [45.5 kB] Get: 333 http://deb.debian.org/debian unstable/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 334 http://deb.debian.org/debian unstable/main arm64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 335 http://deb.debian.org/debian unstable/main arm64 python3-roman all 5.0-1 [10.6 kB] Get: 336 http://deb.debian.org/debian unstable/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 337 http://deb.debian.org/debian unstable/main arm64 python3-greenlet arm64 3.1.0-1+b2 [162 kB] Get: 338 http://deb.debian.org/debian unstable/main arm64 python3-idna all 3.10-1 [42.0 kB] Get: 339 http://deb.debian.org/debian unstable/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 340 http://deb.debian.org/debian unstable/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 341 http://deb.debian.org/debian unstable/main arm64 python3-markupsafe arm64 2.1.5-1+b4 [14.1 kB] Get: 342 http://deb.debian.org/debian unstable/main arm64 python3-jinja2 all 3.1.5-2 [107 kB] Get: 343 http://deb.debian.org/debian unstable/main arm64 python3-mdurl all 0.1.2-1 [9444 B] Get: 344 http://deb.debian.org/debian unstable/main arm64 python3-markdown-it all 3.0.0-2 [62.5 kB] Get: 345 http://deb.debian.org/debian unstable/main arm64 python3-mdit-py-plugins all 0.4.2-1 [32.4 kB] Get: 346 http://deb.debian.org/debian unstable/main arm64 sphinx-common all 8.1.3-5 [617 kB] Get: 347 http://deb.debian.org/debian unstable/main arm64 python3-urllib3 all 2.3.0-1 [114 kB] Get: 348 http://deb.debian.org/debian unstable/main arm64 python3-requests all 2.32.3+dfsg-4 [72.1 kB] Get: 349 http://deb.debian.org/debian unstable/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 350 http://deb.debian.org/debian unstable/main arm64 python3-sphinx all 8.1.3-5 [468 kB] Get: 351 http://deb.debian.org/debian unstable/main arm64 python3-myst-parser all 4.0.1-1 [78.8 kB] Get: 352 http://deb.debian.org/debian unstable/main arm64 python3-pytz all 2025.1-3 [150 kB] Get: 353 http://deb.debian.org/debian unstable/main arm64 python3-tz all 2025.1-3 [4004 B] Get: 354 http://deb.debian.org/debian unstable/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-8+b1 [3872 kB] Get: 355 http://deb.debian.org/debian unstable/main arm64 python3-pandas all 2.2.3+dfsg-8 [3097 kB] Get: 356 http://deb.debian.org/debian unstable/main arm64 python3-pil arm64 11.1.0-5+b1 [495 kB] Get: 357 http://deb.debian.org/debian unstable/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 358 http://deb.debian.org/debian unstable/main arm64 python3-pytest all 8.3.4-1 [250 kB] Get: 359 http://deb.debian.org/debian unstable/main arm64 python3-recommonmark all 0.7.1+ds-8 [17.6 kB] Get: 360 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 361 http://deb.debian.org/debian unstable/main arm64 python3-sqlalchemy all 2.0.32+ds1-1 [1196 kB] Get: 362 http://deb.debian.org/debian unstable/main arm64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Get: 363 http://deb.debian.org/debian unstable/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 364 http://deb.debian.org/debian unstable/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 365 http://deb.debian.org/debian unstable/main arm64 tex-gyre all 20180621-6 [6209 kB] Get: 366 http://deb.debian.org/debian unstable/main arm64 texlive-fonts-recommended all 2024.20250114-1 [4991 kB] Get: 367 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2024.20250114-1 [8760 kB] Get: 368 http://deb.debian.org/debian unstable/main arm64 texlive-pictures all 2024.20250114-1 [17.1 MB] Get: 369 http://deb.debian.org/debian unstable/main arm64 texlive-latex-extra all 2024.20250114-1 [24.7 MB] Fetched 396 MB in 3s (131 MB/s) Preconfiguring packages ... 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Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-markupsafe (2.1.5-1+b4) ... Setting up clang-19 (1:19.1.7-1+b1) ... Setting up libcairo2:arm64 (1.18.2-2) ... Setting up libfreetype-dev:arm64 (2.13.3+dfsg-1) ... Setting up tex-common (6.19) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libxcb-shm0-dev:arm64 (1.17.0-2+b1) ... Setting up python3-roman (5.0-1) ... Setting up python3-jinja2 (3.1.5-2) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up doxygen (1.9.8+ds-2.1) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-certifi (2025.1.31+ds-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up libraqm0:arm64 (0.10.2-1) ... Setting up libpython3.13-dev:arm64 (3.13.2-1) ... Setting up python3-mdurl (0.1.2-1) ... 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Setting up python3-babel (2.17.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up postgresql-client-17 (17.4-1) ... update-alternatives: using /usr/share/postgresql/17/man/man1/psql.1.gz to provide /usr/share/man/man1/psql.1.gz (psql.1.gz) in auto mode Setting up libfontconfig-dev:arm64 (2.15.0-2.1) ... Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.1-1+b1) ... Setting up python3.13-dev (3.13.2-1) ... Setting up python3-pytest (8.3.4-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up preview-latex-style (13.2-1) ... Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-8+b1) ... Setting up python3-mdit-py-plugins (0.4.2-1) ... Setting up python3-yaml (6.0.2-1+b2) ... Setting up debhelper (13.24.1) ... Setting up python3-pytz (2025.1-3) ... Setting up libxaw7:arm64 (2:1.0.16-1) ... Setting up python3-tz (2025.1-3) ... Setting up python3-sqlalchemy (2.0.32+ds1-1) ... Setting up librsvg2-2:arm64 (2.59.90+dfsg-2) ... Setting up python3-pil:arm64 (11.1.0-5+b1) ... Setting up python3-pandas (2.2.3+dfsg-8) ... Setting up python3-dev (3.13.2-2) ... Setting up python3-requests (2.32.3+dfsg-4) ... Setting up libboost-python1.83-dev (1.83.0-4.1+b1) ... Setting up texlive-binaries (2024.20240313.70630+ds-5+b1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up cmake (3.31.6-1) ... Setting up llvm-19 (1:19.1.7-1+b1) ... Setting up llvm-19-tools (1:19.1.7-1+b1) ... Setting up texlive-base (2024.20250114-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up libglib2.0-dev-bin (2.83.5-1) ... Setting up librsvg2-bin (2.59.90+dfsg-2) ... Setting up libboost-python-dev (1.83.0.2+b2) ... Setting up libglib2.0-dev:arm64 (2.83.5-1) ... Setting up texlive-latex-base (2024.20250114-1) ... Setting up texlive-latex-recommended (2024.20250114-1) ... Setting up llvm-19-dev (1:19.1.7-1+b1) ... Setting up texlive-pictures (2024.20250114-1) ... Setting up texlive-fonts-recommended (2024.20250114-1) ... Setting up libcairo2-dev:arm64 (1.18.2-2) ... Setting up latexmk (1:4.86~ds-1) ... Setting up texlive-latex-extra (2024.20250114-1) ... Setting up postgresql-server-dev-17 (17.4-1) ... Setting up postgresql-server-dev-all (274) ... Setting up libheif-plugin-dav1d:arm64 (1.19.5-1+b1) ... Setting up libheif-plugin-libde265:arm64 (1.19.5-1+b1) ... Setting up libheif1:arm64 (1.19.5-1+b1) ... Setting up libmagickcore-7.q16-10:arm64 (8:7.1.1.43+dfsg1-1) ... Setting up libmagickwand-7.q16-10:arm64 (8:7.1.1.43+dfsg1-1) ... Setting up imagemagick-7.q16 (8:7.1.1.43+dfsg1-1) ... update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick.1.gz because associated file /usr/share/man/man1/magick-im7.q16.1.gz (of link group magick) doesn't exist update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick-im7.1.gz because associated file /usr/share/man/man1/magick-im7.q16.1.gz (of link group magick-im7) doesn't exist update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick-script.1.gz because associated file /usr/share/man/man1/magick-script-im7.q16.1.gz (of link group magick-script) doesn't exist update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick-script-im7.1.gz because associated file /usr/share/man/man1/magick-script-im7.q16.1.gz (of link group magick-script-im7) doesn't exist Setting up imagemagick (8:7.1.1.43+dfsg1-1) ... Processing triggers for libc-bin (2.41-4) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-5) ... Setting up python3-myst-parser (4.0.1-1) ... Setting up python3-recommonmark (0.7.1+ds-8) ... Processing triggers for ca-certificates (20241223) ... 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 (6.19) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2068256/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/2068256/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/rdkit-202409.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../rdkit_202409.6-2_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202409.6-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael Banck dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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-202409.6' find /build/reproducible-path/rdkit-202409.6 -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 rm -f -rf /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-* make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6' 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-202409.6' 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_BUILD_INCHI_SUPPORT=ON -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_USE_URF=OFF -DRDK_INSTALL_COMIC_FONTS=OFF -DRDK_BUILD_CAIRO_SUPPORT=ON -DRDK_BUILD_PUBCHEMSHAPE_SUPPORT=OFF -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=/usr -DCATCH_DIR=/usr/include/catch2 -DRDK_BUILD_PGSQL=ON -DRDK_PGSQL_STATIC=OFF -DPostgreSQL_CONFIG=/usr/bin/pg_config -DPostgreSQL_TYPE_INCLUDE_DIR="/usr/include/postgresql/17/server" -DPYTHON_EXECUTABLE=/usr/bin/python3.13 ../ cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/aarch64-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_BUILD_INCHI_SUPPORT=ON -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_USE_URF=OFF -DRDK_INSTALL_COMIC_FONTS=OFF -DRDK_BUILD_CAIRO_SUPPORT=ON -DRDK_BUILD_PUBCHEMSHAPE_SUPPORT=OFF -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=/usr -DCATCH_DIR=/usr/include/catch2 -DRDK_BUILD_PGSQL=ON -DRDK_PGSQL_STATIC=OFF -DPostgreSQL_CONFIG=/usr/bin/pg_config -DPostgreSQL_TYPE_INCLUDE_DIR=/usr/include/postgresql/17/server -DPYTHON_EXECUTABLE=/usr/bin/python3.13 ../ .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Inchi: /usr/lib/aarch64-linux-gnu/libinchi.so -- Found Python3: /usr/bin/python3 (found version "3.13.2") found components: Interpreter Development.Module NumPy Python Install directory /usr/lib/python3.13/site-packages 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 PostgreSQL: /usr/lib/aarch64-linux-gnu/libpq.so (found version "17.4") == Using strict rotor definition -- maeparser include dir set as '/usr/include' -- maeparser libraries set as '/usr/lib/aarch64-linux-gnu/libmaeparser.so' -- coordgen include dir set as /usr/include -- coordgen libraries set as '/usr/lib/aarch64-linux-gnu/libcoordgen.so' -- Found Python3: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Found Cairo: /usr/include/cairo -- Found Freetype: /usr/lib/aarch64-linux-gnu/libfreetype.so (found version "2.13.3") postgres: /usr/include/postgresql;/usr/include/postgresql/17/server CMake Warning (dev) at Code/PgSQL/rdkit/CMakeLists.txt:303 (add_custom_command): Exactly one of PRE_BUILD, PRE_LINK, or POST_BUILD must be given. Assuming POST_BUILD to preserve backward compatibility. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" 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. CMake Warning (dev) at Code/PgSQL/rdkit/CMakeLists.txt:303 (add_custom_command): Exactly one of PRE_BUILD, PRE_LINK, or POST_BUILD must be given. Assuming POST_BUILD to preserve backward compatibility. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" 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. CMake Warning (dev) at Code/PgSQL/rdkit/CMakeLists.txt:303 (add_custom_command): Exactly one of PRE_BUILD, PRE_LINK, or POST_BUILD must be given. Assuming POST_BUILD to preserve backward compatibility. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" 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. -- Configuring done (3.4s) -- Generating done (1.0s) CMake Warning: Manually-specified variables were not used by the project: Boost_NO_BOOST_CMAKE 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 PYTHON_EXECUTABLE -- Build files have been written to: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu for v in $(pg_buildext supported-versions); do \ (mkdir -p Code/PgSQL/rdkit/build-$v && cd Code/PgSQL/rdkit/build-$v && cmake -DPostgreSQL_CONFIG=/usr/lib/postgresql/$v/bin/pg_config -DRDK_PGSQL_STATIC=OFF -DPostgreSQL_TYPE_INCLUDE_DIR="/usr/include/postgresql/$v/server" -DCMAKE_VERBOSE_MAKEFILE=1 -DRDKit_CodeDir=../../../Code ../); \ done -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PostgreSQL: /usr/lib/aarch64-linux-gnu/libpq.so (found version "17.4") postgres: /usr/include/postgresql;/usr/include/postgresql/17/server CMake Warning (dev) at CMakeLists.txt:303 (add_custom_command): Exactly one of PRE_BUILD, PRE_LINK, or POST_BUILD must be given. Assuming POST_BUILD to preserve backward compatibility. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" 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. CMake Warning (dev) at CMakeLists.txt:303 (add_custom_command): Exactly one of PRE_BUILD, PRE_LINK, or POST_BUILD must be given. Assuming POST_BUILD to preserve backward compatibility. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" 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. CMake Warning (dev) at CMakeLists.txt:303 (add_custom_command): Exactly one of PRE_BUILD, PRE_LINK, or POST_BUILD must be given. Assuming POST_BUILD to preserve backward compatibility. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" 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. -- Configuring done (1.1s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-17 make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rdkit-202409.6' dh_auto_build cd obj-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202409.6 -B/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -MF CMakeFiles/rdkitCatch.dir/catch_main.cpp.o.d -o CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/catch_main.cpp [ 1%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/StringChromosome.cpp.o -MF CMakeFiles/ga.dir/ga/StringChromosome.cpp.o.d -o CMakeFiles/ga.dir/ga/StringChromosome.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/GA/ga/StringChromosome.cpp cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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/build/reproducible-path/rdkit-202409.6/Code/ML/Cluster/Murtagh/hc.c cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o -MF CMakeFiles/RDGeneral.dir/utils.cpp.o.d -o CMakeFiles/RDGeneral.dir/utils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/utils.cpp [ 1%] Building CXX object Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDStreams && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RDSTREAMS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDStreams_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o -MF CMakeFiles/RDStreams.dir/streams.cpp.o.d -o CMakeFiles/RDStreams.dir/streams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDStreams/streams.cpp cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK 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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/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o -MF CMakeFiles/RDGeneral.dir/RDLog.cpp.o.d -o CMakeFiles/RDGeneral.dir/RDLog.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDLog.cpp [ 1%] Built target coordgen_support [ 1%] Built target inchi_support [ 1%] Built target ringdecomposerlib_support [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -MF CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o.d -o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/LocaleSwitcher.cpp [ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/Chromosome.cpp.o cd 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-fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/Chromosome.cpp.o -MF CMakeFiles/ga.dir/ga/Chromosome.cpp.o.d -o CMakeFiles/ga.dir/ga/Chromosome.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/GA/ga/Chromosome.cpp [ 1%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-202409.6/Code/ML/Cluster/Murtagh/hcdriver.c [ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/External/GA/ga/IntegerStringChromosomePolicy.cpp [ 1%] Linking C shared library ../../../../lib/libRDKithc.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wl,--dependency-file=CMakeFiles/hc.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKithc.so.1 -o ../../../../lib/libRDKithc.so.1.2024.09.6 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2024.09.6 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o -MF CMakeFiles/RDGeneral.dir/versions.cpp.o.d -o CMakeFiles/RDGeneral.dir/versions.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/versions.cpp [ 1%] Built target hc [ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/External/GA/util/RandomUtil.cpp [ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/util/Util.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o -MF CMakeFiles/testDict.dir/testDict.cpp.o.d -o CMakeFiles/testDict.dir/testDict.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/testDict.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/FPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/FPBReader.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/FPBReader.cpp [ 3%] Linking CXX executable testConcurrentQueue cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConcurrentQueue.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/RealValueVect.cpp.o -MF CMakeFiles/DataStructs.dir/RealValueVect.cpp.o.d -o CMakeFiles/DataStructs.dir/RealValueVect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/RealValueVect.cpp make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd 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../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 7%] Built target testMatCalc [ 7%] Linking CXX shared library ../../lib/libRDKitCatalogs.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Catalogs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2024.09.6 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 7%] Built target Catalogs [ 7%] Linking CXX executable testMatrices cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMatrices.dir/link.d CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 7%] Built target testMatrices [ 7%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script 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/build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Geometry /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake "--color=" make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu 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'/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake "--color=" make -f Code/DataStructs/CMakeFiles/catchDataStructs.dir/build.make Code/DataStructs/CMakeFiles/catchDataStructs.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/CMakeFiles/catchDataStructs.dir/DependInfo.cmake "--color=" make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/DataStructs/testDatastructs.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/Geometry/Transform2D.cpp [ 7%] Building CXX object 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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 -MD -MT Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -MF CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o.d -o CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/testMultiFPB.cpp cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -MF CMakeFiles/testFPB.dir/testFPB.cpp.o.d -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/testFPB.cpp [ 8%] Building CXX object Code/DataStructs/CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK 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Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMetricMatrixCalc_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 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-I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ML/InfoTheory/InfoBitRanker.cpp [ 9%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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 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/usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/SimDivPickers/Wrap/MaxMinPicker.cpp [ 12%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. 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&& /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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDGeometryLib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 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/UniformRealValueGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 14%] 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol 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CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp [ 14%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/cQuantize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so 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-I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd 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-o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/testTransforms.cpp [ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp [ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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_BitOps.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/wrap_BitOps.cpp [ 14%] Linking CXX shared library ../../../lib/libRDKitAlignment.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 [ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Bond.cpp [ 16%] Linking CXX executable testConrec cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConrec.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong 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-c /build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap/UniformRealValueGrid3D.cpp [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolOps.cpp [ 17%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FindRings.cpp [ 17%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdAlignment.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 17%] Built target rdAlignment [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/ROMol.cpp.o -MF CMakeFiles/GraphMol.dir/ROMol.cpp.o.d -o CMakeFiles/GraphMol.dir/ROMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ROMol.cpp [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/RWMol.cpp [ 17%] Linking CXX executable testChemicalFeatures cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testChemicalFeatures.dir/link.d 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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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/PeriodicTable.cpp [ 18%] Built target testChemicalFeatures [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/atomic_data.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/QueryOps.cpp /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FindRings.cpp:1292:36: warning: unused parameter 'mol' [-Wunused-parameter] 1292 | void findRingFamilies(const ROMol &mol) { | ~~~~~~~~~~~~~^~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/bits/stl_tree.h:63, from /usr/include/c++/14/map:62, from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PeriodicTable.h:14, from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PeriodicTable.cpp:11: /usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PeriodicTable.cpp:96:57: required from here 96 | adata.d_isotopeInfoMap[isotope] = std::make_pair(mass, abundance); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ [ 18%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdGeometry.cpp.o -MF CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o.d -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap/rdGeometry.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolPickler.cpp.o -MF CMakeFiles/GraphMol.dir/MolPickler.cpp.o.d -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolPickler.cpp [ 18%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/cDataStructs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DataStructs/cDataStructs.so CMakeFiles/cDataStructs.dir/DataStructs.cpp.o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 18%] Built target cDataStructs [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Canon.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/AtomIterators.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/BondIterators.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -MF CMakeFiles/GraphMol.dir/Aromaticity.cpp.o.d -o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Aromaticity.cpp /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolPickler.cpp: In function 'void RDKit::streamReadPositiveChar(std::istream&, char&, int)': /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolPickler.cpp:72:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 72 | if (res < 0) { | ~~~~^~~ [ 18%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 18%] Built target rdGeometry [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Kekulize.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/AddHs.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Matrices.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Chirality.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/RingInfo.cpp [ 19%] Linking CXX shared module ../../../rdkit/rdBase.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdBase.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 19%] Built target rdBase [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o cd 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-I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Renumber.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS 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19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Resonance.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/StereoGroup.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/new_canon.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SubstanceGroup.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FindStereo.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MonomerInfo.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/NontetrahedralStereo.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atropisomers.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Atropisomers.cpp.o -MF CMakeFiles/GraphMol.dir/Atropisomers.cpp.o.d -o CMakeFiles/GraphMol.dir/Atropisomers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Atropisomers.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/WedgeBonds.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolProps.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolProps.cpp.o -MF CMakeFiles/GraphMol.dir/MolProps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolProps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProps.cpp [ 20%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/GraphMol.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2024.09.6 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/Atropisomers.cpp.o CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o CMakeFiles/GraphMol.dir/MolProps.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1 ../../lib/libRDKitGraphMol.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 20%] Built target GraphMol make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make 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'/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f 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-o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmilesParse.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/tableTestsCatch.dir/DependInfo.cmake "--color=" [ 21%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o [ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGenericGroups_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERICGROUPS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -MF CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o.d -o CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GenericGroups/GenericGroups.cpp cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/SmilesParseOps.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmilesParseOps.cpp [ 21%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o [ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Trajectory/Trajectory.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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"--color=" [ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CIPMol.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/CIPMol.cpp [ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SmilesParse/SmartsWrite.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/tableTestsCatch.dir/build.make 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CIPLabeler.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/CIPLabeler.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 21%] Building CXX object Code/GraphMol/CMakeFiles/tableTestsCatch.dir/catch_periodictable.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/tableTestsCatch.dir/catch_periodictable.cpp.o -MF CMakeFiles/tableTestsCatch.dir/catch_periodictable.cpp.o.d -o CMakeFiles/tableTestsCatch.dir/catch_periodictable.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_periodictable.cpp [ 21%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/GasteigerCharges.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/GasteigerCharges.cpp [ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Mancude.cpp [ 21%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Trajectory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2024.09.6 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 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/build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 21%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/Digraph.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tableTestsCatch.dir/link.d CMakeFiles/tableTestsCatch.dir/catch_periodictable.cpp.o -o tableTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitGraphMol.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 21%] Built target tableTestsCatch make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 22%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolInterchange/Parser.cpp [ 22%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/PartialCharges/GasteigerParams.cpp [ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -MF CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/CXSmilesOps.cpp [ 22%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Subgraphs/SubgraphUtils.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o cd 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-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-202409.6/Code/GraphMol/CIPLabeler/Node.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o -MF CMakeFiles/CIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Edge.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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CMakeFiles/CIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Sort.cpp [ 24%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolCatalog/MolCatalogParams.cpp [ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CanonicalizeStereoGroups.cpp.o -MF CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o.d -o CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/CanonicalizeStereoGroups.cpp [ 24%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 [ 24%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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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24%] Built target MolTransforms make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build /usr/bin/c++ -fPIC -g -O2 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'/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so [ 24%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/SLNParse.cpp.o -MF CMakeFiles/SLNParse.dir/SLNParse.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/SLNParse.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 24%] Built target PartialCharges make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdqueries.cpp.o -MF CMakeFiles/rdqueries.dir/rdqueries.cpp.o.d -o CMakeFiles/rdqueries.dir/rdqueries.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/rdqueries.cpp [ 24%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 [ 24%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/GenericGroups.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGenericGroups.so.1 -o ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2024.09.6 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2024.09.6 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so [ 24%] Built target GenericGroups make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o [ 24%] Built target MolCatalog cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Trajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Trajectory.cpp 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap 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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 -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdChemicalFeatures.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/configs/Configuration.cpp [ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SmilesParse/smarts.tab.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp [ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SmilesParse/smiles.tab.cpp [ 24%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Subgraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 24%] Built target Subgraphs make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct 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-I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp [ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Tetrahedral.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && 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Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp [ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SmilesParse/lex.yysmarts.cpp [ 25%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/rdTrajectory.cpp [ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SLNParse/SLNAttribs.cpp [ 26%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp [ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp [ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp [ 27%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdChemicalFeatures.dir/link.d -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.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 27%] Built target rdChemicalFeatures 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake "--color=" [ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-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-202409.6/Code/Numerics/Optimizer/LinearSearch.cpp [ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION 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-DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Substruct/SubstructUtils.cpp make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend make[4]: Entering directory 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Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp [ 28%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra 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'/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 28%] Built target Optimizer make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' [ 28%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 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/build/reproducible-path/rdkit-202409.6/Code/ForceField/ForceField.cpp [ 28%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SLNParse/sln.tab.cpp [ 28%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 [ 28%] Linking CXX executable testOptimizer cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testOptimizer.dir/link.d CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 28%] Built target testOptimizer make -f 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object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/AngleConstraint.cpp.o -MF CMakeFiles/ForceField.dir/AngleConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraint.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/AngleConstraints.cpp.o -MF CMakeFiles/ForceField.dir/AngleConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraints.cpp [ 31%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -MF CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o.d -o CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/memtest1.cpp [ 31%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -MF CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o.d -o CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_queries.cpp [ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o cd 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraint.cpp [ 31%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 [ 31%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolInterchange.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2024.09.6 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2024.09.6 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/usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 31%] Built target MolInterchange make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/depend [ 31%] Built target rdqueries make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o -MF CMakeFiles/smiTest2.dir/test2.cpp.o.d -o CMakeFiles/smiTest2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/test2.cpp [ 31%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/v2catch_tests.cpp.o -MF CMakeFiles/v2smiTestCatch.dir/v2catch_tests.cpp.o.d -o CMakeFiles/v2smiTestCatch.dir/v2catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/v2catch_tests.cpp [ 31%] Linking CXX executable graphmolcpTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/DistanceConstraints.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraints.cpp [ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/PositionConstraint.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o -c 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../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 31%] Built target SubstructMatch make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend make[4]: Entering directory 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o -MF CMakeFiles/testSubgraphs2.dir/test2.cpp.o.d -o CMakeFiles/testSubgraphs2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs/test2.cpp [ 31%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs/catch_tests.cpp [ 32%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SLNParse/lex.yysln.cpp [ 32%] Linking CXX executable graphmolIterTest cd 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/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 32%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp [ 32%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/PartialCharges/test1.cpp [ 32%] Linking CXX executable graphmolMemTest1 cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/AngleBend.cpp [ 32%] Linking CXX executable queryTestsCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/queryTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall 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-D_FORTIFY_SOURCE=2 -Wdate-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/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -MF CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o.d -o CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp [ 33%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 [ 33%] Linking CXX executable testPartialCharges cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPartialCharges.dir/link.txt --verbose=1 [ 33%] Linking CXX executable subgraphsCatch cd 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 33%] Built target testPartialCharges 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -MF CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o.d -o CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp [ 33%] Built target subgraphsCatch make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake "--color=" [ 33%] Linking CXX executable testSubgraphs1 cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs1.dir/link.txt --verbose=1 [ 33%] Built target SLNParse make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend make[4]: Leaving directory 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -MF CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o.d -o CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/Abbreviations.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 33%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -MF CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o.d -o CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/querytest.cpp [ 33%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp [ 33%] Linking CXX executable testSubgraphs2 cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs2.dir/link.txt --verbose=1 [ 33%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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-DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ForceField/UFF/Params.cpp [ 34%] Linking CXX shared module 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../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 34%] Built target rdShapeHelpers make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix 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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-202409.6/Code/GraphMol/Fingerprints/Fingerprints.cpp [ 34%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ReducedGraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitReducedGraphs.so.1 -o 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o -MF CMakeFiles/smaTest1.dir/smatest.cpp.o.d -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/smatest.cpp [ 34%] Linking CXX executable moliteratorTestsCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/moliteratorTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro 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-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-202409.6/Code/GraphMol/ReducedGraphs/test1.cpp [ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Utils.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/Utils.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Utils.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Utils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Utils.cpp [ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 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../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 34%] Built target rdMolInterchange make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap 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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 -DrdReducedGraphs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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-I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/FragCatalogEntry.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp [ 34%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK 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CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o.d -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp [ 34%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp [ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o.d -o 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../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 34%] Built target MolAlign make -f 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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 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o -MF CMakeFiles/testSLNParse.dir/test.cpp.o.d -o CMakeFiles/testSLNParse.dir/test.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/test.cpp [ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp [ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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ForceFields::MMFF::MMFFStbn*)': /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/StretchBend.cpp:27:35: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 27 | const MMFFStbn *mmffStbnParams) { | ^ [ 34%] Linking CXX executable graphmolqueryTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolqueryTest.dir/link.d CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest 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CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp [ 36%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ForceField/MMFF/TorsionAngle.cpp [ 36%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK 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CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatParams.cpp [ 36%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ForceField/MMFF/Nonbonded.cpp [ 36%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2024.09.6 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 36%] Built target MolChemicalFeatures make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp [ 37%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 37%] Built target rdSLNParse [ 37%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FragCatalog/FragFPGenerator.cpp [ 37%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Depictor/EmbeddedFrag.cpp [ 37%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK 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CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganFingerprints.cpp [ 37%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Fingerprints/AtomPairs.cpp [ 37%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-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-202409.6/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp [ 37%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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/usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 37%] Built target rdCoordGen [ 37%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp [ 37%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FragCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2024.09.6 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/ChemicalFeatureUtils.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp [ 38%] Linking CXX shared library ../../lib/libRDKitForceField.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 [ 38%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Fingerprints/MACCS.cpp [ 38%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp [ 38%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Depictor/DepictUtils.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2024.09.6 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/UFF/Utils.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp [ 39%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdAbbreviations.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp [ 40%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp [ 40%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolChemicalFeatures.so 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 40%] Built target rdMolChemicalFeatures [ 40%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MorganGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.cpp [ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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-I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/FingerprintUtil.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/FingerprintUtil.cpp /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp: In function 'void RDKit::MMFF::Tools::addStretchBend(const RDKit::ROMol&, RDKit::MMFF::MMFFMolProperties*, ForceFields::ForceField*)': /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp:419:68: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 419 | MMFF::Utils::calcStbnForceConstants(&mmffStbnParams); | ^ [ 40%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp [ 40%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o cd 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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp [ 40%] Linking CXX shared library ../../../lib/libRDKitDepictor.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Depictor.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2024.09.6 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o 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Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ChemTransforms/MolFragmenter.cpp [ 40%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so [ 40%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 40%] Built target Fingerprints make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 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-DrdFingerprintGenerator_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 40%] Built target FilterCatalog make -f 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-I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp [ 41%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp [ 41%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 [ 41%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ForceFieldHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 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 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../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 41%] Built target ForceFieldHelpers make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/depend make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ForceField /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DistGeom /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ForceField/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolHash.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2024.09.6 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2024.09.6 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so [ 41%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o cd 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-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-202409.6/Code/DistGeom/DistGeomUtils.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 41%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ForceField/Wrap/ForceField.cpp [ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/catch_tests.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 41%] Built target MolHash make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceFieldHelpers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp [ 41%] Linking CXX shared library ../../lib/libRDKitRDInchiLib.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDInchiLib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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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cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDInchiLib.so.1.2024.09.6 ../../lib/libRDKitRDInchiLib.so.1 ../../lib/libRDKitRDInchiLib.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 41%] Built target RDInchiLib 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap 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-DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolHash_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp [ 42%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/TriangleSmooth.cpp.o -MF CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o.d -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/TriangleSmooth.cpp [ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdDepictor.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 42%] Built target rdDepictor make -f Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/build.make Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/build.make Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 42%] Building CXX object Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolInteractionFields_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERACTIONFIELDS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o -MF CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o.d -o CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/MIFDescriptors.cpp [ 43%] Linking CXX executable ForceFieldsCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ForceFieldsCatch.dir/link.d CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -o ForceFieldsCatch ../RDGeneral/librdkitCatch.a 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Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/ChiralViolationContribs.cpp [ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolHash.dir/link.d 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 43%] Built target rdMolHash [ 43%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DistGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2024.09.6 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 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'/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' [ 43%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o [ 43%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ 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Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/DistGeom/Wrap/DistGeom.cpp [ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat 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../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 43%] Built target rdForceFieldHelpers [ 43%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FileParsers/CDXMLParser.cpp [ 44%] Linking CXX shared module ../../../rdkit/Chem/rdinchi.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/INCHI-API/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdinchi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/Mol2FileParser.cpp [ 44%] Linking CXX executable testDistGeom cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDistGeom.dir/link.d CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 44%] Built target testDistGeom [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FileParsers/MolFileParser.cpp [ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 [ 44%] Linking CXX shared library ../../../lib/libRDKitMolInteractionFields.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInteractionFields.dir/link.txt --verbose=1 [ 44%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMHFPFingerprint.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolInteractionFields.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInteractionFields.so.1 -o ../../../lib/libRDKitMolInteractionFields.so.1.2024.09.6 CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl [ 44%] Built target rdMHFPFingerprint cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInteractionFields.so.1.2024.09.6 ../../../lib/libRDKitMolInteractionFields.so.1 ../../../lib/libRDKitMolInteractionFields.so [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FileParsers/MolSGroupParsing.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 44%] Built target MolInteractionFields make -f Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build.make Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build.make Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 45%] Building CXX object Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMIF_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o -MF CMakeFiles/rdMIF.dir/rdMIF.cpp.o.d -o CMakeFiles/rdMIF.dir/rdMIF.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/Wrap/rdMIF.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 45%] Built target rdForceField [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FileParsers/MolSGroupWriting.cpp [ 45%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 [ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/DistGeom.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 45%] Built target DistGeom [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FileParsers/MolFileStereochem.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdFingerprintGenerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 46%] Built target rdFingerprintGenerator [ 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FileParsers/SDWriter.cpp [ 46%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DistGeomHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 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'/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 46%] Built target DistGeomHelpers [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/SmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD 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46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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-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-202409.6/Code/GraphMol/FileParsers/TplFileParser.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION 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-I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FileParsers/PDBWriter.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/XYZFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/XYZFileWriter.cpp [ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdMIF.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMIF.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat 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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -MF CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/SequenceWriters.cpp [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FileParsers/SVGParser.cpp [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/PNGParser.cpp.o -MF CMakeFiles/FileParsers.dir/PNGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/PNGParser.cpp [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp [ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdfiltercatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 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../../../lib/libRDKitChemTransforms.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E 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'/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake "--color=" make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol 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'/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build [ 48%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/UFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -MF CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o.d -o CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/testUFFForceField.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend [ 48%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -MF CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o.d -o CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/testMMFFForceField.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build [ 49%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o [ 49%] Building CXX object 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o -MF CMakeFiles/graphmolTest1.dir/test1.cpp.o.d -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/test1.cpp cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -MF CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o.d -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/molopstest.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -MF CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o.d -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/testChirality.cpp make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend [ 50%] Building CXX object 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-DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -MF CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o.d -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c 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/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 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/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT 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-I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -MF CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o.d -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/resMolSupplierTest.cpp [ 50%] Building CXX object Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/testMolBundle.cpp [ 51%] Building CXX object Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o -MF CMakeFiles/testSGroup.dir/testSGroup.cpp.o.d -o CMakeFiles/testSGroup.dir/testSGroup.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/testSGroup.cpp [ 51%] Linking CXX executable molBundleTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -MF CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o.d -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/test-valgrind.cpp [ 51%] Linking CXX executable resMolSupplierTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 51%] Built target resMolSupplierTest make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -MF 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'/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -MF CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o.d -o CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/nontetrahedral_tests.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Built target graphmoltestPickler make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor 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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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o -MF CMakeFiles/testDepictor.dir/testDepictor.cpp.o.d -o CMakeFiles/testDepictor.dir/testDepictor.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/testDepictor.cpp [ 53%] Linking CXX executable molopsTestsCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molopsTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molopsTestsCatch.dir/link.d CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -o molopsTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 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-DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -MF CMakeFiles/depictorCatch.dir/catch_tests.cpp.o.d -o 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../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Built target pickleTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make 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'/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o -MF CMakeFiles/fileParsersTest1.dir/test1.cpp.o.d -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/test1.cpp [ 53%] Linking CXX executable canonTestsCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/canonTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/canonTestsCatch.dir/link.d CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -o canonTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Built target canonTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/testAtropisomers.dir/testAtropisomers.cpp.o -MF CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o.d -o CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testAtropisomers.cpp [ 53%] Linking CXX executable graphmoltestChirality cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestChirality.dir/link.d CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Built target graphmoltestChirality make -f Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -MF CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o.d -o CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testSquiggleDoubleBonds.cpp [ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MDLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MDLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/MDLParser.cpp [ 53%] Linking CXX executable nontetrahedralCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/nontetrahedralCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nontetrahedralCatch.dir/link.d CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -o nontetrahedralCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Built target nontetrahedralCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 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/usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 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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-202409.6/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp [ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDepictor.dir/link.d CMakeFiles/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 54%] Built target testDepictor 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o cd 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionPickler.cpp [ 55%] Linking CXX executable testGeneralFileReader cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGeneralFileReader.dir/link.d CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitRDStreams.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Built target testGeneralFileReader make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o -MF CMakeFiles/testTplParser.dir/testTpls.cpp.o.d -o CMakeFiles/testTplParser.dir/testTpls.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testTpls.cpp [ 55%] Linking CXX executable testMultithreadedMolSupplier cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMultithreadedMolSupplier.dir/link.d CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitRDStreams.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Built target testMultithreadedMolSupplier 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/FileParsers/testMol2ToMol.cpp [ 55%] Linking CXX executable graphmolTestsCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolTestsCatch.dir/link.d CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Built target graphmolTestsCatch 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix 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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/FileParsers/testSequence.cpp [ 55%] Linking CXX executable testTplParser cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testTplParser.dir/link.d CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Built target testTplParser make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp [ 55%] Linking CXX executable testMol2ToMol cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMol2ToMol.dir/link.d CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Built target testMol2ToMol make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/FileParsers/file_parsers_catch.cpp [ 55%] Linking CXX executable testSequence cd 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../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Built target testSequence make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd 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-std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -MF CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o.d -o CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testPropertyLists.cpp [ 55%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/ReactionWriter.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionWriter.cpp [ 55%] Linking CXX executable chiralityTestsCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/chiralityTestsCatch.dir/link.d CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitCIPLabeler.so.1.2024.09.6 ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Built target chiralityTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd 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/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -MF CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o.d -o CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/XYZFileParserCatchTest.cpp [ 55%] Linking CXX executable smiTest1 cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smiTest1.dir/link.d 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp [ 55%] Linking CXX executable depictorCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong 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../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Built target depictorCatch 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp [ 55%] Linking CXX executable testExtendedStereoParsing cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 [ 55%] Linking CXX executable testMolSupplier cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testExtendedStereoParsing.dir/link.d CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Built target testExtendedStereoParsing 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/FileParsers/connectTheDots_catch.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolSupplier.dir/link.d CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitRDStreams.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Built target testMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -MF CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o.d -o CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/v2_suppliers_catch.cpp [ 55%] Linking CXX executable testMolWriter cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolWriter.dir/link.d CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Built target testMolWriter make -f Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build.make 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'/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -MF CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o.d -o CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/v2_file_parsers_catch.cpp [ 55%] Linking CXX executable smiTestCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smiTestCatch.dir/link.d CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Built target smiTestCatch make -f Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu 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CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/multithreaded_supplier_catch.cpp [ 55%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/ReactionDepict.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionDepict.cpp [ 55%] Linking CXX executable connectTheDotsTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/connectTheDotsTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/Substruct/test1.cpp [ 55%] Linking CXX executable XYZFileParserCatchTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/XYZFileParserCatchTest.dir/link.d CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -o XYZFileParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/catch_tests.cpp [ 55%] Linking CXX executable v2MolSuppliers cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2MolSuppliers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemTransforms/testChemTransforms.cpp [ 55%] Linking CXX executable v2FileParsersCatchTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2FileParsersCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2FileParsersCatchTest.dir/link.d CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -o v2FileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a 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-I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemTransforms/catch_tests.cpp cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/ReactionFingerprints.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp [ 56%] Linking CXX executable molfileStereoCatchTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/molfileStereoCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molfileStereoCatchTest.dir/link.d CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -o molfileStereoCatchTest 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-DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -MF CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o.d -o CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp [ 56%] Linking CXX executable cdxmlParserCatchTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/cdxmlParserCatchTest.dir/link.d CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -o cdxmlParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 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directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o -MF CMakeFiles/testFragCatalog.dir/test1.cpp.o.d -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/test1.cpp [ 56%] Linking CXX executable multithreadedSupplierCatchTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/multithreadedSupplierCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Descriptors/Crippen.cpp [ 57%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ 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-Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionUtils.cpp [ 57%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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-I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/Fingerprints/test1.cpp [ 57%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Descriptors/BCUT.cpp [ 57%] Linking CXX executable testFragCatalog cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFragCatalog.dir/link.d CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 57%] Built target testFragCatalog make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp [ 57%] Linking CXX executable graphmolMolOpsTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolMolOpsTest.dir/link.d CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 57%] Built target graphmolMolOpsTest 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -MF CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o.d -o CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp [ 57%] Linking CXX executable substructTestCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructTestCatch.dir/link.d CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 57%] Built target substructTestCatch make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/Fingerprints/catch_tests.cpp [ 57%] Linking CXX executable testSubstructMatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSubstructMatch.dir/link.d CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 57%] Built target testSubstructMatch 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -MF CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o.d -o CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/BCUT.cpp: In function 'std::pair RDKit::Descriptors::{anonymous}::BCUT2D(std::unique_ptr >&, const std::vector&)': /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/BCUT.cpp:70:71: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 70 | const std::vector &atom_props) { | ^ [ 58%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionRunner.cpp [ 58%] Linking CXX executable fileParsersTest1 cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E 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-DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/MolTransforms/test1.cpp [ 58%] Linking CXX executable testMHFPFingerprint cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMHFPFingerprint.dir/link.d CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -o testMHFPFingerprint ../../../lib/libRDKitFingerprints.so.1.2024.09.6 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/PreprocessRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/PreprocessRxn.cpp [ 58%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK 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-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-202409.6/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp [ 58%] Linking CXX executable chemTransformsTestCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemTransformsTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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-DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/molTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/catch_tests.cpp [ 58%] Linking CXX executable testChemTransforms cd 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Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp [ 58%] Linking CXX executable molTransformsTestCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTransformsTestCatch.dir/link.txt --verbose=1 [ 58%] Linking CXX executable testMolTransforms cd 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 58%] Built target molTransformsTestCatch make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend [ 58%] Built target testMolTransforms make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp [ 58%] Linking CXX executable fpGenTestCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fpGenTestCatch.dir/link.d CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -o fpGenTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp [ 58%] Linking CXX executable forceFieldHelpersCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/forceFieldHelpersCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/forceFieldHelpersCatch.dir/link.d CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -o forceFieldHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 58%] Built target forceFieldHelpersCatch make -f 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -MF CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o.d -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp [ 58%] Linking CXX executable fpTestCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fpTestCatch.dir/link.d CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -o fpTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 58%] Built target fpTestCatch 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -MF CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o.d -o CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp [ 58%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Descriptors/MolDescriptors.cpp [ 58%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -MF CMakeFiles/ChemReactions.dir/PNGParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/PNGParser.cpp [ 58%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CDXMLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/CDXMLParser.cpp [ 58%] Linking CXX executable fileParsersCatchTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileParsersCatchTest.dir/link.d CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -o fileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 58%] Built target fileParsersCatchTest 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/DistGeomHelpers/catch_tests.cpp [ 59%] Linking CXX executable testMMFFForceFieldHelpersMultiThread cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.d CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o testMMFFForceFieldHelpersMultiThread ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 59%] Built target testMMFFForceFieldHelpersMultiThread make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake "--color=" [ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Descriptors/MolSurf.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_MAX_ARITY=32 -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDistGeom_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp [ 60%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp [ 60%] Linking CXX executable testFingerprintGenerators cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFingerprintGenerators.dir/link.d CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 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'/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -MF CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o.d -o CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/testMolAlign.cpp [ 60%] Linking CXX executable testCrystalForceField cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCrystalForceField.dir/link.d CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 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/build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp [ 60%] Linking CXX executable testFingerprints cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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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/usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 60%] Built target testFingerprints make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures 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-DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp [ 60%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so cd 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/usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 60%] Built target rdfragcatalog make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -MF CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o.d -o CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp [ 60%] Linking CXX executable testMMFFForceFieldHelpers cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceFieldHelpers.dir/link.d CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 60%] Built target testMMFFForceFieldHelpers make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog 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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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/MolCatalog/test1.cpp [ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Descriptors/Lipinski.cpp [ 60%] Linking CXX executable molAlignCatchTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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-I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/FMCS.cpp.o -MF CMakeFiles/FMCS.dir/FMCS.cpp.o.d -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/FMCS.cpp [ 60%] Linking CXX executable testUFFForceFieldHelpers cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong 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-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-202409.6/Code/GraphMol/MolHash/catch_tests.cpp [ 60%] Linking CXX executable testMolAlign cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolAlign.dir/link.d 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o -MF CMakeFiles/MMPA.dir/MMPA.cpp.o.d -o CMakeFiles/MMPA.dir/MMPA.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/MMPA.cpp [ 60%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp [ 60%] Linking CXX executable testShapeHelpers cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testShapeHelpers.dir/link.d 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/usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 60%] Built target testShapeHelpers make -f Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/RascalMCES.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalMCES.cpp [ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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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-202409.6/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp [ 60%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 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/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearch_details.cpp [ 60%] Linking CXX executable testMolCatalog cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat 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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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -MF CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o.d -o CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Trajectory/trajectoryTest.cpp [ 60%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpace.cpp [ 60%] Linking CXX executable distGeomHelpersCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -MF CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o.d -o CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/catch_tests.cpp [ 61%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -MF CMakeFiles/Descriptors.dir/MQN.cpp.o.d -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MQN.cpp [ 62%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ChemReactions.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemReactions.so.1 -o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 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/usr/lib/aarch64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 62%] Built target ChemReactions make -f Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Seed.cpp.o -MF CMakeFiles/FMCS.dir/Seed.cpp.o.d -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Seed.cpp [ 62%] Linking CXX shared library ../../../lib/libRDKitMMPA.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2024.09.6 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 62%] Built target MMPA make -f Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/build.make Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields 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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/testMIF.cpp [ 62%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSet.cpp [ 63%] Linking CXX executable molHashCatchTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinParser.cpp [ 63%] Linking CXX executable trajectoryTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp [ 64%] Linking CXX executable molInterchangeTest1 cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt 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CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinWriter.cpp [ 64%] Linking CXX executable molInterchangeCatchTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molInterchangeCatchTest.dir/link.d CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -o molInterchangeCatchTest ../../RDGeneral/librdkitCatch.a 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/usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 64%] Built target molInterchangeCatchTest make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend [ 64%] Linking CXX executable testAbbreviations cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAbbreviations.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu 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testReactionFingerprints cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testReactionFingerprints.dir/link.d CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -o testReactionFingerprints ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 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'/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 64%] Built target testReactionFingerprints make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 64%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolDraw2D.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.cpp [ 64%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinDefs.cpp [ 64%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.cpp [ 64%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSubstructureSearcher.cpp [ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/USRDescriptor.cpp.o -MF CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o.d -o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/USRDescriptor.cpp [ 65%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/RascalMCES/RascalButinaCluster.cpp [ 65%] Linking CXX executable testEnumeration cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong 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../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 65%] Built target testEnumeration 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/MMPA/MMPA_UnitTest.cpp [ 65%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/SubstructMatchCustom.cpp.o -MF CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o.d -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/SubstructMatchCustom.cpp In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/bits/stl_tree.h:63, from /usr/include/c++/14/map:62, from /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/Dict.h:19, from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h:16, from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:16: /usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:768:42: required from here 768 | auto new_mins = getAtomCoords(make_pair(x_min, y_min)); | ~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ [ 65%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o -MF CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o.d -o CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/lap_a_la_scipy.cpp [ 65%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -MF CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o.d -o CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/PartitionSet.cpp [ 65%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalResult.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/RascalResult.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalResult.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalResult.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalResult.cpp [ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Descriptors/AtomFeat.cpp [ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/OxidationNumbers.cpp.o -MF CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o.d -o CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/OxidationNumbers.cpp [ 66%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.cpp [ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DCLV.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/DCLV.cpp.o -MF CMakeFiles/Descriptors.dir/DCLV.cpp.o.d -o CMakeFiles/Descriptors.dir/DCLV.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/DCLV.cpp [ 66%] Linking CXX shared library ../../../lib/libRDKitFMCS.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FMCS.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2024.09.6 CMakeFiles/FMCS.dir/FMCS.cpp.o CMakeFiles/FMCS.dir/Seed.cpp.o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 66%] Built target FMCS make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/Wrap 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-DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -MF CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o.d -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp [ 66%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolStandardize.cpp.o -MF CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o.d -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/MolStandardize.cpp [ 66%] Linking CXX executable testMMPA cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMPA.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection 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../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 66%] Built target testMMPA make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu 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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.cpp [ 67%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp [ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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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-202409.6/Code/GraphMol/Descriptors/EEM.cpp [ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Descriptors/PBF.cpp [ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Descriptors/PMI.cpp [ 67%] Linking CXX shared library ../../../lib/libRDKitSynthonSpaceSearch.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/SynthonSpaceSearch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SynthonSpaceSearch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSynthonSpaceSearch.so.1 -o ../../../lib/libRDKitSynthonSpaceSearch.so.1.2024.09.6 CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSynthonSpaceSearch.so.1.2024.09.6 ../../../lib/libRDKitSynthonSpaceSearch.so.1 ../../../lib/libRDKitSynthonSpaceSearch.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 67%] Built target SynthonSpaceSearch make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make 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Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDeprotect_EXPORTS -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Deprotect/Deprotect.cpp [ 67%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 67%] Built target rdMMPA make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap 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Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o -MF CMakeFiles/rdmolops.dir/rdmolops.cpp.o.d -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/rdmolops.cpp [ 67%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/PositionVariation.cpp.o -MF CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o.d -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/PositionVariation.cpp [ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ 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-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-202409.6/Code/GraphMol/Descriptors/AUTOCORR3D.cpp [ 67%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolStandardize/Metal.cpp [ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ 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-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-202409.6/Code/GraphMol/Descriptors/RDF.cpp [ 67%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -MF CMakeFiles/rdmolops.dir/MolOps.cpp.o.d -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MolOps.cpp [ 67%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o cd 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp [ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MORSE.cpp.o -MF CMakeFiles/Descriptors.dir/MORSE.cpp.o.d -o CMakeFiles/Descriptors.dir/MORSE.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MORSE.cpp [ 67%] Linking CXX shared library ../../../lib/libRDKitRascalMCES.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/RascalMCES.dir/link.txt --verbose=1 [ 67%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/Deprotect.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RascalMCES.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRascalMCES.so.1 -o ../../../lib/libRDKitRascalMCES.so.1.2024.09.6 CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o CMakeFiles/RascalMCES.dir/RascalResult.cpp.o ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRascalMCES.so.1.2024.09.6 ../../../lib/libRDKitRascalMCES.so.1 ../../../lib/libRDKitRascalMCES.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 67%] Built target RascalMCES make -f Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDeprotect.so.1.2024.09.6 ../../../lib/libRDKitDeprotect.so.1 ../../../lib/libRDKitDeprotect.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 67%] Built target Deprotect make -f Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/build.make Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu 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-std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o -MF CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o.d -o CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/Wrap/rdMolProcessing.cpp [ 67%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MarvinParser.dir/link.d -Wl,-z,relro -Wl,-z,now 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cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 67%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ 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-I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Descriptors/GETAWAY.cpp [ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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-I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -MF CMakeFiles/Descriptors.dir/CoulombMat.cpp.o.d -o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/CoulombMat.cpp [ 69%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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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/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-202409.6/Code/GraphMol/MolEnumerator/LinkNode.cpp [ 69%] Linking CXX executable testMolProcessing cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolProcessing.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro 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Linking CXX shared module ../../../../rdkit/Chem/rdMolProcessing.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolProcessing.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolProcessing.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolProcessing.so CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o ../../../../lib/libRDKitMolProcessing.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 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/usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 70%] Built target rdMolProcessing make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu 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CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Validate.cpp.o -MF CMakeFiles/MolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Validate.cpp [ 70%] Linking CXX executable FMCStest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 70%] Built target FMCStest make -f Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build.make Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap 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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/Wrap/rdRascalMCES.cpp [ 70%] Linking CXX executable testRascalCluster cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRascalCluster.dir/link.d CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -o testRascalCluster ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 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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-202409.6/Code/GraphMol/MolEnumerator/RepeatUnit.cpp [ 70%] Linking CXX executable testFMCS cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFMCS.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFMCS.dir/link.d CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.so.1.2024.09.6 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-DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/Deprotect/deprotectTest.cpp [ 71%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdFMCS.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 71%] Built target rdFMCS 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/Wrap 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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 -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp [ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolStandardize/Charge.cpp [ 72%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp [ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdRascalMCES.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRascalMCES.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Table.cpp.o -MF CMakeFiles/rdchem.dir/Table.cpp.o.d -o CMakeFiles/rdchem.dir/Table.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Table.cpp [ 72%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 [ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdSynthonSpaceSearch.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSynthonSpaceSearch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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-I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -MF CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o.d -o CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp [ 75%] Linking CXX executable testReaction cd 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/Descriptors/test.cpp [ 75%] Linking CXX executable testMrvToMol cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o -MF CMakeFiles/testEEM.dir/testEEM.cpp.o.d -o CMakeFiles/testEEM.dir/testEEM.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testEEM.cpp [ 75%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK 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/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Node.cpp In file included from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: /usr/include/boost/smart_ptr/shared_ptr.hpp:459:66: warning: '*(const boost::shared_ptr*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)).boost::shared_ptr::px' may be used uninitialized [-Wmaybe-uninitialized] 459 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) | ~~^~ /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/shared_ptr.hpp:18: In copy constructor 'boost::detail::shared_count::shared_count(const boost::detail::shared_count&)', inlined from 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]' at /usr/include/boost/smart_ptr/shared_ptr.hpp:459:72, inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: /usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: '((const boost::detail::shared_count*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)))[1].boost::detail::shared_count::pi_' may be used uninitialized [-Wmaybe-uninitialized] 438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) | ~~^~~ /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: /usr/include/boost/smart_ptr/shared_ptr.hpp:459:66: warning: '*(const boost::shared_ptr*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)).boost::shared_ptr::px' may be used uninitialized [-Wmaybe-uninitialized] 459 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) | ~~^~ /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In copy constructor 'boost::detail::shared_count::shared_count(const boost::detail::shared_count&)', inlined from 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]' at /usr/include/boost/smart_ptr/shared_ptr.hpp:459:72, inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: /usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: '((const boost::detail::shared_count*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)))[1].boost::detail::shared_count::pi_' may be used uninitialized [-Wmaybe-uninitialized] 438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) | ~~^~~ /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 77%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 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../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 81%] Built target testAUTOCORR3D make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator 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-DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -MF CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o.d -o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/enumerator_catch.cpp [ 81%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp [ 81%] Linking CXX executable testCoulombMat cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCoulombMat.dir/link.d CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 81%] Built target testCoulombMat make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend [ 81%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/MaeMolSupplier.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 81%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolEnumerator_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -MF CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o.d -o CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp: In function 'std::pair {anonymous}::{anonymous}::BCUT2D_list(const RDKit::ROMol&, boost::python::list)': /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:444:61: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 444 | python::list atomprops) { | ^ [ 81%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/AtropisomerBond.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp [ 81%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp In file included from /usr/include/c++/14/vector:62, from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1022:38, inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: /usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' writing between 5 and 9223372036854775804 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/vector:63: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1013:40, inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset [-9223372036854775808, -1] into destination object of size [4, 9223372036854775804] allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 81%] Linking CXX executable descriptorsTestCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/descriptorsTestCatch.dir/link.d CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 81%] Built target descriptorsTestCatch [ 81%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolDraw2D/DrawShape.cpp [ 81%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolDraw2D/DrawText.cpp [ 81%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp [ 82%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp [ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/RingInfo.cpp [ 83%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/O3AAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2024.09.6 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2024.09.6 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 83%] Built target O3AAlign make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 83%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -MF CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o.d -o CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/testO3AAlign.cpp [ 83%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/string:51, from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawText.h:19, from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawText.cpp:13: /usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawText.cpp:165:47: required from here 165 | tl = mol_draw.getAtomCoords(std::make_pair(tl.x, tl.y)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ [ 83%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/CIPLabeler/rules/Rule2.cpp [ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/MaeWriter.cpp [ 84%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -MF 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-I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp [ 85%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so cd 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/usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 85%] Built target rdMolEnumerator make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu 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-DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -MF CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o.d -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp [ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/string:51, from /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/Invariant.h:17, from /build/reproducible-path/rdkit-202409.6/Code/Numerics/Matrix.h:14, from /build/reproducible-path/rdkit-202409.6/Code/Numerics/SquareMatrix.h:14, from /build/reproducible-path/rdkit-202409.6/Code/Geometry/Transform3D.h:16, from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/AlignMolecules.h:14, from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/testO3AAlign.cpp:11: /usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/testO3AAlign.cpp:643:37: required from here 643 | oscores.push_back(std::make_pair(rmsd, score)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ [ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp [ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolDraw2D/DrawTextJS.cpp [ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT 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CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DCairo.cpp [ 86%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule3.cpp [ 86%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD 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-I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/EditableMol.cpp [ 86%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MonomerInfo.cpp.o -MF CMakeFiles/rdchem.dir/MonomerInfo.cpp.o.d -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MonomerInfo.cpp [ 86%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp [ 87%] Linking CXX executable testMolEnumerator cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection 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../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 87%] Built target testMolEnumerator [ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ 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-Wdate-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-202409.6/Code/GraphMol/MolDraw2D/DrawTextCairo.cpp [ 87%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp [ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o cd 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/SDMolSupplier.cpp [ 87%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK 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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule5.cpp [ 87%] Linking CXX executable testO3AAlign cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testO3AAlign.dir/link.d CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2024.09.6 ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 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../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 87%] Built target testO3AAlign [ 87%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolDraw2D/DrawTextFT.cpp [ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o.d -o 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-I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule6.cpp [ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp [ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o cd 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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/StereoGroup.cpp [ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/SubstanceGroup.cpp [ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/TautomerCatalog/TautomerCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp [ 89%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 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cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o -MF CMakeFiles/rdchem.dir/Chirality.cpp.o.d -o CMakeFiles/rdchem.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Chirality.cpp [ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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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-202409.6/Code/GraphMol/Wrap/SmilesMolSupplier.cpp [ 89%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 [ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 89%] Built target rdMolDescriptors [ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/SmilesWriter.cpp [ 89%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolDraw2D.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolDraw2D.so.1 -o ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libfreetype.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcairo.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 89%] Built target MolDraw2D make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -MF CMakeFiles/moldraw2DTest1.dir/test1.cpp.o.d -o CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/test1.cpp make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/catch_tests.cpp In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3906, from /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/types.h:21, from /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/utils.h:15, from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/test1.cpp:12: /usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/test1.cpp:1592:46: required from here 1592 | drawer.getAtomCoords(std::make_pair(ocoords.x, ocoords.y)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -MF CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o.d -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/rxn_test1.cpp make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build [ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/SDWriter.cpp [ 89%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_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 -DrdMolDraw2D_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -MF CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o.d -o 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-I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/TDTWriter.cpp [ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/PDBWriter.cpp [ 89%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so make[4]: Leaving directory 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/MolStandardize/test1.cpp [ 91%] Linking CXX executable moldraw2DRxnTest1 cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script 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/usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 91%] Built target moldraw2DRxnTest1 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/MolStandardize/testNormalize.cpp 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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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-202409.6/Code/GraphMol/MolStandardize/testValidate.cpp make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -MF CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o.d -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/testTautomer.cpp [ 91%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong 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-I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/MolStandardize/test2.cpp [ 91%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 make -f 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/MolStandardize/testFragment.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdchem.dir/link.d -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.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 91%] Built target rdchem 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 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-I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/molStandardizePipelineTest.dir/testPipeline.cpp.o -MF CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o.d -o CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/testPipeline.cpp [ 91%] Linking CXX executable molNormalizeTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 /usr/bin/c++ 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Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 91%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp [ 91%] Linking CXX executable molStandardizeTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 91%] Built target molStandardizeTest make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend make[4]: Entering 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Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SCAFFOLDNETWORK_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp [ 92%] Linking CXX executable molValidateTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 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-DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp [ 92%] Linking CXX executable molStandardizeSmallTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizeSmallTest.dir/link.d 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-DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGeneralizedSubstruct_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERALIZEDSUBSTRUCT_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/GeneralizedSubstruct/XQMol.cpp [ 92%] Linking CXX executable molFragmentTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molFragmentTest.dir/link.d CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -o molFragmentTest 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CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp [ 92%] Linking CXX executable moldraw2DTest1 cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DTest1.dir/link.d CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 92%] Built target moldraw2DTest1 [ 92%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2024.09.6 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 92%] Built target ScaffoldNetwork make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' [ 92%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/GeneralizedSubstruct/TextIO.cpp [ 92%] Linking CXX executable molTautomerTest cd 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../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 92%] Built target molTautomerTest make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make 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-DRDK_USE_STRICT_ROTOR_DEFINITION -DrdScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp [ 92%] Linking CXX executable tautomerQueryTestCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tautomerQueryTestCatch.dir/link.d CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 92%] Built target tautomerQueryTestCatch [ 92%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Charge.cpp [ 93%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp [ 93%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so cd 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/usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 93%] Built target rdTautomerQuery [ 93%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp [ 94%] Linking CXX executable molStandardizePipelineTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizePipelineTest.dir/link.txt --verbose=1 [ 94%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 94%] Built target molStandardizePipelineTest [ 94%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolStandardize/Wrap/Metal.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolDraw2D.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 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../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 94%] Built target rdMolDraw2D [ 94%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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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-202409.6/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp [ 96%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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&& /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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CMakeFiles/rdkit.dir/adapter.cpp.o.d -o CMakeFiles/rdkit.dir/adapter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp [ 96%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SubstructLibrary/PatternFactory.cpp [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o -MF CMakeFiles/rdkit.dir/bfp_op.c.o.d -o CMakeFiles/rdkit.dir/bfp_op.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/bfp_op.c [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o -MF CMakeFiles/rdkit.dir/cache.c.o.d -o CMakeFiles/rdkit.dir/cache.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/cache.c [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o -MF CMakeFiles/rdkit.dir/guc.c.o.d -o CMakeFiles/rdkit.dir/guc.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/guc.c [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o -MF CMakeFiles/rdkit.dir/low_gist.c.o.d -o CMakeFiles/rdkit.dir/low_gist.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/low_gist.c 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-202409.6/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 = long int]', inlined from 'boost::python::extract::operator result_type() const [with T = long int]' at /usr/include/boost/python/extract.hpp:136:23, inlined from 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:617:27: /usr/include/boost/python/extract.hpp:185:11: warning: '*(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 | ); | ^ In file included from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12: /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]': /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:617:27: note: '' declared here 617 | long to = extract( slice->stop); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = long int]', inlined from 'boost::python::extract::operator result_type() const [with T = long int]' at /usr/include/boost/python/extract.hpp:136:23, inlined from 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:603:29: /usr/include/boost/python/extract.hpp:185:11: warning: '*(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 | ); | ^ /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]': /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:603:29: note: '' declared here 603 | long from = extract( slice->start); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o -MF CMakeFiles/rdkit.dir/mol_op.c.o.d -o CMakeFiles/rdkit.dir/mol_op.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/mol_op.c [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_gist.c.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_gist.c.o -MF CMakeFiles/rdkit.dir/rdkit_gist.c.o.d -o CMakeFiles/rdkit.dir/rdkit_gist.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/rdkit_gist.c [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o -MF CMakeFiles/rdkit.dir/bfp_gist.c.o.d -o CMakeFiles/rdkit.dir/bfp_gist.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/bfp_gist.c [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gin.c.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gin.c.o -MF CMakeFiles/rdkit.dir/bfp_gin.c.o.d -o CMakeFiles/rdkit.dir/bfp_gin.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/bfp_gin.c [ 97%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT 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-Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o -MF CMakeFiles/rdkit.dir/rdkit_io.c.o.d -o CMakeFiles/rdkit.dir/rdkit_io.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/rdkit_io.c [ 97%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rxn_op.c.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rxn_op.c.o -MF CMakeFiles/rdkit.dir/rxn_op.c.o.d -o CMakeFiles/rdkit.dir/rxn_op.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/rxn_op.c [ 97%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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int bitFlags) { | ~~~~~~~~~~~~~^~~~~~~~ [ 97%] Linking CXX executable moldraw2DTestCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DTestCatch.dir/link.d CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitCIPLabeler.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 97%] Built target rdMolStandardize [ 97%] Linking CXX executable generalizedSubstructCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/generalizedSubstructCatch.dir/link.txt --verbose=1 [ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeneralizedSubstruct.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 97%] Built target rdGeneralizedSubstruct /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/generalizedSubstructCatch.dir/link.d CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -o generalizedSubstructCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 97%] Built target generalizedSubstructCatch [ 97%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 97%] Built target SubstructLibrary make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/depend make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' [ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -MF CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o.d -o CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp [ 98%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/SubstructLibrary/catch_tests.cpp [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp [ 99%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 99%] 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[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 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-I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make 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-I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -MF CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o.d -o CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp [ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o cd 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-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -MF CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o.d -o CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/catch_rgd.cpp [ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp [ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/GaExample.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/gaExample.dir/GaExample.cpp.o -MF CMakeFiles/gaExample.dir/GaExample.cpp.o.d -o CMakeFiles/gaExample.dir/GaExample.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/GaExample.cpp [ 99%] Linking CXX shared library librdkit.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkit.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/rdkit.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,librdkit.so -o librdkit.so CMakeFiles/rdkit.dir/adapter.cpp.o CMakeFiles/rdkit.dir/bfp_op.c.o CMakeFiles/rdkit.dir/cache.c.o CMakeFiles/rdkit.dir/guc.c.o CMakeFiles/rdkit.dir/low_gist.c.o CMakeFiles/rdkit.dir/mol_op.c.o CMakeFiles/rdkit.dir/rdkit_gist.c.o CMakeFiles/rdkit.dir/bfp_gist.c.o CMakeFiles/rdkit.dir/bfp_gin.c.o CMakeFiles/rdkit.dir/bitstring.c.o CMakeFiles/rdkit.dir/rdkit_io.c.o CMakeFiles/rdkit.dir/rxn_op.c.o CMakeFiles/rdkit.dir/sfp_op.c.o -L/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/lib /usr/lib/aarch64-linux-gnu/libpq.so ../../../lib/libRDKitRDInchiLib.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libinchi.so ../../../lib/libRDKitMolInterchange.so.1.2024.09.6 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitMolHash.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/sql /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit/sql cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/data /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit/data cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/expected /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit/expected make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 99%] Built target rdkit [ 99%] Linking CXX executable testRGroupDecompInternals cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 [ 99%] Linking CXX executable gaExample cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/gaExample.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecompInternals.dir/link.d CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 99%] Built target testRGroupDecompInternals /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gaExample.dir/link.d CMakeFiles/gaExample.dir/GaExample.cpp.o -o gaExample ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 99%] Built target gaExample [ 99%] Linking CXX executable substructLibraryTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryTest.dir/link.d CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 99%] Built target substructLibraryTest [ 99%] Linking CXX executable substructLibraryCatchTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryCatchTest.dir/link.d CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 99%] Built target substructLibraryCatchTest [ 99%] Linking CXX executable testSynthonSpaceSubstructureSearch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.txt --verbose=1 /usr/bin/ld: CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o: in function `CATCH2_INTERNAL_TEST_20()': ./obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/./Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp:306:(.text+0x72b0): warning: the use of `tmpnam' is dangerous, better use `mkstemp' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.d CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -o testSynthonSpaceSubstructureSearch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 99%] Built target testSynthonSpaceSubstructureSearch [ 99%] Linking CXX executable rgroupCatchTests cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/rgroupCatchTests.dir/link.d CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 99%] Built target rgroupCatchTests [ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdRGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../../lib/libRDKitga.so.1.2024.09.6 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 99%] Built target rdRGroupDecomposition [ 99%] Linking CXX executable testRGroupDecomp cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecomp.dir/link.d CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 99%] Built target testRGroupDecomp [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o ../../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [100%] Built target rdSubstructLibrary make[3]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' for v in $(pg_buildext supported-versions); do \ (cd Code/PgSQL/rdkit/build-$v && make || $(cat ../../../../obj-*/Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/link.txt | sed -e 's#\.\./\.\./#../../../../obj-*/Code/#g')); \ done make[2]: Entering directory '/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-17' /usr/bin/cmake -S/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit -B/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-17 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-17/CMakeFiles /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-17//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-17' make -f CMakeFiles/rdkit.dir/build.make CMakeFiles/rdkit.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-17' cd /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-17 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-17 /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-17 /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-17/CMakeFiles/rdkit.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-17' make -f CMakeFiles/rdkit.dir/build.make CMakeFiles/rdkit.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-17' [ 7%] Building CXX object CMakeFiles/rdkit.dir/adapter.cpp.o /usr/bin/c++ -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/adapter.cpp.o -MF CMakeFiles/rdkit.dir/adapter.cpp.o.d -o CMakeFiles/rdkit.dir/adapter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp [ 14%] Building C object CMakeFiles/rdkit.dir/bfp_op.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/bfp_op.c.o -MF CMakeFiles/rdkit.dir/bfp_op.c.o.d -o CMakeFiles/rdkit.dir/bfp_op.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/bfp_op.c [ 21%] Building C object CMakeFiles/rdkit.dir/cache.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/cache.c.o -MF CMakeFiles/rdkit.dir/cache.c.o.d -o CMakeFiles/rdkit.dir/cache.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/cache.c [ 28%] Building C object CMakeFiles/rdkit.dir/guc.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/guc.c.o -MF CMakeFiles/rdkit.dir/guc.c.o.d -o CMakeFiles/rdkit.dir/guc.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/guc.c [ 35%] Building C object CMakeFiles/rdkit.dir/low_gist.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/low_gist.c.o -MF CMakeFiles/rdkit.dir/low_gist.c.o.d -o CMakeFiles/rdkit.dir/low_gist.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/low_gist.c [ 42%] Building C object CMakeFiles/rdkit.dir/mol_op.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/mol_op.c.o -MF CMakeFiles/rdkit.dir/mol_op.c.o.d -o CMakeFiles/rdkit.dir/mol_op.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/mol_op.c [ 50%] Building C object CMakeFiles/rdkit.dir/rdkit_gist.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/rdkit_gist.c.o -MF CMakeFiles/rdkit.dir/rdkit_gist.c.o.d -o CMakeFiles/rdkit.dir/rdkit_gist.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/rdkit_gist.c [ 57%] Building C object CMakeFiles/rdkit.dir/bfp_gist.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/bfp_gist.c.o -MF CMakeFiles/rdkit.dir/bfp_gist.c.o.d -o CMakeFiles/rdkit.dir/bfp_gist.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/bfp_gist.c [ 64%] Building C object CMakeFiles/rdkit.dir/bfp_gin.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/bfp_gin.c.o -MF CMakeFiles/rdkit.dir/bfp_gin.c.o.d -o CMakeFiles/rdkit.dir/bfp_gin.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/bfp_gin.c [ 71%] Building C object CMakeFiles/rdkit.dir/bitstring.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/bitstring.c.o -MF CMakeFiles/rdkit.dir/bitstring.c.o.d -o CMakeFiles/rdkit.dir/bitstring.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/bitstring.c [ 78%] Building C object CMakeFiles/rdkit.dir/rdkit_io.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/rdkit_io.c.o -MF CMakeFiles/rdkit.dir/rdkit_io.c.o.d -o CMakeFiles/rdkit.dir/rdkit_io.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/rdkit_io.c [ 85%] Building C object CMakeFiles/rdkit.dir/rxn_op.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/rxn_op.c.o -MF CMakeFiles/rdkit.dir/rxn_op.c.o.d -o CMakeFiles/rdkit.dir/rxn_op.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/rxn_op.c [ 92%] Building C object CMakeFiles/rdkit.dir/sfp_op.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/sfp_op.c.o -MF CMakeFiles/rdkit.dir/sfp_op.c.o.d -o CMakeFiles/rdkit.dir/sfp_op.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/sfp_op.c [100%] Linking CXX shared library librdkit.so /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkit.dir/link.txt --verbose=1 /usr/bin/ld: cannot find -lGeneralizedSubstruct: No such file or directory /usr/bin/ld: cannot find -lMolEnumerator: No such file or directory /usr/bin/ld: cannot find -lTautomerQuery: No such file or directory /usr/bin/ld: cannot find -lMolDraw2D: No such file or directory /usr/bin/ld: cannot find -lMolTransforms: No such file or directory /usr/bin/ld: cannot find -lMolHash: No such file or directory /usr/bin/ld: cannot find -lFMCS: No such file or directory /usr/bin/ld: cannot find -lChemReactions: No such file or directory /usr/bin/ld: cannot find -lChemTransforms: No such file or directory /usr/bin/ld: cannot find -lFileParsers: No such file or directory /usr/bin/ld: cannot find -lSmilesParse: No such file or directory /usr/bin/ld: cannot find -lFingerprints: No such file or directory /usr/bin/ld: cannot find -lSubgraphs: No such file or directory /usr/bin/ld: cannot find -lDescriptors: No such file or directory /usr/bin/ld: cannot find -lPartialCharges: No such file or directory /usr/bin/ld: cannot find -lSubstructMatch: No such file or directory /usr/bin/ld: cannot find -lGraphMol: No such file or directory /usr/bin/ld: cannot find -lEigenSolvers: No such file or directory /usr/bin/ld: cannot find -lDataStructs: No such file or directory /usr/bin/ld: cannot find -lDepictor: No such file or directory /usr/bin/ld: cannot find -lRDGeometryLib: No such file or directory /usr/bin/ld: cannot find -lRDGeneral: No such file or directory /usr/bin/ld: cannot find -lrdkit_base: No such file or directory collect2: error: ld 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-lFingerprints -lSubgraphs -lDescriptors -lPartialCharges -lSubstructMatch -lGraphMol -lEigenSolvers -lDataStructs -lDepictor -lRDGeometryLib -lRDGeneral -lrdkit_base make[4]: *** [CMakeFiles/rdkit.dir/build.make:297: librdkit.so] Error 1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-17' make[3]: *** [CMakeFiles/Makefile2:90: CMakeFiles/rdkit.dir/all] Error 2 make[3]: Leaving directory '/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-17' make[2]: *** [Makefile:139: all] Error 2 make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-17' (cd /build/reproducible-path/rdkit-202409.6/Code; doxygen doxygen/doxygen.config) warning: Tag 'TCL_SUBST' at line 213 of file 'doxygen/doxygen.config' has become obsolete. 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directory /build/reproducible-path/rdkit-202409.6/Code/RDBoost Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/DistGeom Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/ForceField Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/Numerics Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/Numerics/Optimizer Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/Numerics/EigenSolvers Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/Geometry Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/Features Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures Reading and parsing tag files Parsing files Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/Abbreviations.h... 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Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/SanitizeRxn.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/SanitizeRxn.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemTransforms/ChemTransforms.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemTransforms/ChemTransforms.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemTransforms/MolFragmenter.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemTransforms/MolFragmenter.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Chirality.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Chirality.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/CIPLabeler.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/CIPLabeler.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/CIPMol.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/CIPMol.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Configuration.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Configuration.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Sp2Bond.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Sp2Bond.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Descriptor.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Descriptor.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Digraph.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Digraph.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Edge.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Edge.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Mancude.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Mancude.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Node.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Node.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Priority.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Priority.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Pairlist.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Pairlist.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1a.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1a.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1b.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1b.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule2.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule2.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule3.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule3.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4a.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4a.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4b.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4b.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4c.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4c.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule5.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule5.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule5New.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule5New.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule6.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule6.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rules.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rules.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/SequenceRule.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/SequenceRule.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Sort.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Sort.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/TooManyNodesException.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/TooManyNodesException.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Conformer.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Conformer.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/DepictUtils.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/DepictUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/EmbeddedFrag.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/EmbeddedFrag.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/RDDepictor.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/RDDepictor.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/Templates.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/Templates.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/TemplateSmiles.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/TemplateSmiles.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect/Deprotect.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect/Deprotect.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/AtomFeat.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/AtomFeat.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/AUTOCORR2D.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/AUTOCORR2D.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/AUTOCORR3D.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/AUTOCORR3D.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/BCUT.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/BCUT.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/ConnectivityDescriptors.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/ConnectivityDescriptors.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/CoulombMat.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/CoulombMat.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Crippen.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Crippen.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Data3Ddescriptors.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Data3Ddescriptors.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/DCLV.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/DCLV.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/EEM.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/EEM.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/GETAWAY.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/GETAWAY.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Lipinski.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Lipinski.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolDescriptors.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolDescriptors.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolDescriptors3D.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolDescriptors3D.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolSurf.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolSurf.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MORSE.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MORSE.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MQN.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MQN.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/OxidationNumbers.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/OxidationNumbers.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/PBF.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/PBF.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/PMI.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/PMI.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Property.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Property.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/RDF.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/RDF.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/RegisterDescriptor.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/RegisterDescriptor.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/USRDescriptor.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/USRDescriptor.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/WHIM.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/WHIM.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/details.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/details.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DetermineBonds/DetermineBonds.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DetermineBonds/DetermineBonds.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/Embedder.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/Embedder.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/CDXMLParser.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/CDXMLParser.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileParsers.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileParsers.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileParserUtils.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileParserUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/GeneralFileReader.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/GeneralFileReader.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MaestroProperties.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MaestroProperties.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolFileStereochem.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolFileStereochem.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSGroupParsing.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSGroupParsing.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSGroupWriting.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSGroupWriting.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.v1API.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.v1API.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolWriters.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolWriters.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/PNGParser.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/PNGParser.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/ProximityBonds.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/ProximityBonds.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/SequenceParsers.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/SequenceParsers.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/SequenceWriters.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/SequenceWriters.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterCatalog.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterCatalog.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatchers.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatchers.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Filters.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Filters.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/AtomPairGenerator.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/AtomPairGenerator.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/AtomPairs.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/AtomPairs.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/FingerprintGenerator.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/FingerprintGenerator.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Fingerprints.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Fingerprints.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/FingerprintUtil.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/FingerprintUtil.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MACCS.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MACCS.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MHFP.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MHFP.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganFingerprints.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganFingerprints.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/RDKitFPGenerator.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/RDKitFPGenerator.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Composition2N.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Composition2N.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/DebugTrace.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/DebugTrace.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/FMCS.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/FMCS.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Graph.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Graph.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/MatchTable.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/MatchTable.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Seed.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Seed.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/SeedSet.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/SeedSet.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/SubstructMatchCustom.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/SubstructMatchCustom.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/SubstructureCache.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/SubstructureCache.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Target.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Target.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/TargetMatch.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/TargetMatch.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/FFConvenience.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/FFConvenience.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatGenerator.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatGenerator.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatParams.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatParams.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragFPGenerator.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragFPGenerator.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/XQMol.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/XQMol.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GenericGroups/GenericGroups.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GenericGroups/GenericGroups.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GraphMol.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GraphMol.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinDefs.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinDefs.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinParser.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinParser.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/MMPA.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/MMPA.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/AlignMolecules.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/AlignMolecules.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolBundle.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolBundle.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/MolCatalog.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/MolCatalog.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/MolCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/MolCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/AtomSymbol.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/AtomSymbol.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawAnnotation.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawAnnotation.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMol.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMol.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCH.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCH.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawShape.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawShape.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawText.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawText.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextCairo.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextCairo.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFT.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFT.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTCairo.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Dr/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.h:233: warning: unbalanced grouping commands awTextFTCairo.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTJS.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTJS.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTSVG.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTSVG.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextJS.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextJS.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextNotFT.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextNotFT.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextSVG.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextSVG.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Fonts/roboto_regular.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Fonts/roboto_regular.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Fonts/telex_regular.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Fonts/telex_regular.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DJS.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DJS.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Qt/DrawTextFTQt.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Qt/DrawTextFTQt.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Qt/DrawTextQt.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Qt/DrawTextQt.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Qt/MolDraw2DQt.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Qt/MolDraw2DQt.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/StringRect.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/StringRect.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/LinkNode.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/LinkNode.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h... Prepro/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolOps.h:489: warning: unbalanced grouping commands /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolOps.h:747: warning: unbalanced grouping commands cessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/mf.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/mf.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/MolHash.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/MolHash.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/nmmolhash.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/nmmolhash.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/MIFDescriptors.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/MIFDescriptors.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/details.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/details.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/MolInterchange.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/MolInterchange.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolOps.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolOps.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolPickler.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolPickler.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/MolProcessing.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/MolProcessing.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Charge.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Charge.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Fragment.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Fragment.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Metal.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Metal.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/MolStandardize.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/MolStandardize.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Normalize.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Normalize.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Pipeline.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Pipeline.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Tautomer.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Tautomer.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Validate.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Validate.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/MolTransforms.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/MolTransforms.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MonomerInfo.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MonomerInfo.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/new_canon.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/new_canon.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/GasteigerCharges.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/GasteigerCharges.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/GasteigerParams.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/GasteigerParams.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PeriodicTable.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PeriodicTable.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryAtom.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryAtom.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryBond.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryBond.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/PartitionSet.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/PartitionSet.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalClusterOptions.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalClusterOptions.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalDetails.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalDetails.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalMCES.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalMCES.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalOptions.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalOptions.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalResult.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalResult.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RDKitBase.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RDKitBase.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RDKitQueries.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RDKitQueries.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs/ReducedGraphs.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs/ReducedGraphs.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Resonance.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Resonance.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupCore.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupCore.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupData.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupData.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupGa.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupGa.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupMatch.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupMatch.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupScore.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupScore.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupUtils.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RingInfo.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RingInfo.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Rings.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Rings.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ROMol.h... Parsing file /build/reproducible-path/rdkit-202409.6//build/reproducible-path/rdkit-202409.6/Code/GraphMol/ROMol.h:416: warning: unbalanced grouping commands Code/GraphMol/ROMol.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RWMol.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RWMol.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SanitException.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SanitException.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/detail.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/detail.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/SLNAttribs.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/SLNAttribs.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/SLNParse.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/SLNParse.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/SLNParseOps.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/SLNParseOps.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/CanonicalizeStereoGroups.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/CanonicalizeStereoGroups.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmartsWrite.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmartsWrite.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmilesParse.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmilesParse.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmilesParseOps.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmilesParseOps.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmilesWrite.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmilesWrite.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StereoGroup.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StereoGroup.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/Pattern.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/Pattern.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/ReCharge.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/ReCharge.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/Stereo.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/Stereo.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/StripSmallFragments.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/StripSmallFragments.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/StructChecker.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/StructChecker.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/StructCheckerOptions.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/StructCheckerOptions.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/Tautomer.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/Tautomer.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/Utilites.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/Utilites.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs/Subgraphs.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs/Subgraphs.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs/SubgraphUtils.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs/SubgraphUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstanceGroup.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstanceGroup.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/SubstructMatch.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/SubstructMatch.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/SubstructUtils.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/SubstructUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/PatternFactory.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/PatternFactory.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SearchResults.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SearchResults.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/Synthon.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/Synthon.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSet.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSet.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpace.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpace.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearch_details.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearch_details.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSubstructureSearcher.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSubstructureSearcher.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery/TautomerQuery.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery/TautomerQuery.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Trajectory/Snapshot.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Trajectory/Snapshot.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Trajectory/Trajectory.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Trajectory/Trajectory.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Catalogs/Catalog.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Catalogs/Catalog.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Catalogs/CatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Catalogs/CatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Catalogs/CatalogParams.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Catalogs/CatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/base64.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataStructs/base64.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitOps.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitOps.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitVect.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitVect.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitVects.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitVects.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitVectUtils.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitVectUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/DatastructsException.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataStructs/DatastructsException.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/DatastructsStreamOps.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataStructs/DatastructsStreamOps.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/DiscreteDistMat.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataStructs/DiscreteDistMat.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/DiscreteValueVect.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataStructs/DiscreteValueVect.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/ExplicitBitVect.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataStructs/ExplicitBitVect.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/FPBReader.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataStructs/FPBReader.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/MultiFPBReader.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataStructs/MultiFPBReader.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/RealValueVect.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataStructs/RealValueVect.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/SparseBitVect.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataStructs/SparseBitVect.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/SparseIntVect.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataStructs/SparseIntVect.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Query/AndQuery.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Query/AndQuery.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Query/EqualityQuery.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Query/EqualityQuery.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Query/GreaterEqualQuery.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Query/GreaterEqualQuery.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Query/GreaterQuery.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Query/GreaterQuery.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Query/LessEqualQuery.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Query/LessEqualQuery.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Query/LessQuery.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Query/LessQuery.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Query/NullQueryAlgebra.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Query/NullQueryAlgebra.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Query/OrQuery.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Query/OrQuery.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Query/Query.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Query/Query.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Query/QueryObjects.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Query/QueryObjects.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Query/RangeQuery.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Query/RangeQuery.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Query/SetQuery.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Query/SetQuery.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Query/XOrQuery.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Query/XOrQuery.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory/CorrMatGenerator.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory/CorrMatGenerator.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory/InfoBitRanker.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory/InfoBitRanker.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory/InfoGainFuncs.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory/InfoGainFuncs.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataManip/MetricMatrixCalc/MetricFuncs.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataManip/MetricMatrixCalc/MetricFuncs.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/DistPicker.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/DistPicker.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/HierarchicalClusterPicker.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/HierarchicalClusterPicker.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/LeaderPicker.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/LeaderPicker.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/MaxMinPicker.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/MaxMinPicker.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/BadFileException.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/BadFileException.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/BoostEndInclude.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/BoostEndInclude.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/BoostStartInclude.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/BoostStartInclude.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/ConcurrentQueue.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/ConcurrentQueue.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/ControlCHandler.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/ControlCHandler.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/Dict.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/Dict.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/Exceptions.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/Exceptions.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/export.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/export.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/FileParseException.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/FileParseException.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/hanoiSort.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/hanoiSort.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/Invariant.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/Invariant.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/LocaleSwitcher.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/LocaleSwitcher.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/Ranking.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/Ranking.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDAny.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDAny.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDConfig.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDConfig.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDExportMacros.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDExportMacros.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDLog.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDLog.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDProps.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDProps.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDThreads.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDThreads.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDValue-doublemagic.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDValue-doublemagic.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDValue-taggedunion.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDValue-taggedunion.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDValue.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDValue.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/StreamOps.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/StreamOps.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/types.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/types.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/utils.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/utils.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/versions.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/versions.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDBoost/boost_numpy.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDBoost/boost_numpy.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDBoost/import_array.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDBoost/import_array.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDBoost/pyint_api.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDBoost/pyint_api.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDBoost/PySequenceHolder.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDBoost/PySequenceHolder.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDBoost/python.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDBoost/python.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDBoost/python_streambuf.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/RDBoost/python_streambuf.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DistGeom/BoundsMatrix.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DistGeom/BoundsMatrix.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DistGeom/ChiralSet.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DistGeom/ChiralSet.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DistGeom/ChiralViolationContrib.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DistGeom/ChiralViolationContrib.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DistGeom/ChiralViolationContribs.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DistGeom/ChiralViolationContribs.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DistGeom/DistGeomUtils.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DistGeom/DistGeomUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DistGeom/DistViolationContrib.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DistGeom/DistViolationContrib.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DistGeom/DistViolationContribs.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DistGeom/DistViolationContribs.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DistGeom/FourthDimContrib.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DistGeom/FourthDimContrib.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DistGeom/FourthDimContribs.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DistGeom/FourthDimContribs.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DistGeom/TriangleSmooth.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/DistGeom/TriangleSmooth.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraints.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraints.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/Contrib.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/Contrib.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraints.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraints.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/ForceField.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/ForceField.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/AngleBend.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/AngleBend.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/AngleConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/AngleConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/BondStretch.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/BondStretch.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/Contribs.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/Contribs.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/DistanceConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/DistanceConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/Nonbonded.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/Nonbonded.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/OopBend.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/OopBend.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/Params.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/Params.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/PositionConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/PositionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/StretchBend.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/StretchBend.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/TorsionAngle.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/TorsionAngle.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/TorsionConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/TorsionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/PositionConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/PositionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/TorsionConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/TorsionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/AngleBend.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/AngleBend.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/AngleConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/AngleConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/BondStretch.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/BondStretch.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Contribs.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Contribs.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/DistanceConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/DistanceConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Inversion.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Inversion.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Inversions.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Inversions.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Nonbonded.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Nonbonded.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Params.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Params.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/PositionConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/PositionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/TorsionAngle.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/TorsionAngle.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/TorsionConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/TorsionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Utils.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Utils.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment/AlignPoints.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment/AlignPoints.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Numerics/Conrec.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Numerics/Conrec.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Numerics/Matrix.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Numerics/Matrix.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Numerics/Optimizer/BFGSOpt.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Numerics/Optimizer/BFGSOpt.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Numerics/SquareMatrix.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Numerics/SquareMatrix.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Numerics/SymmMatrix.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Numerics/SymmMatrix.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Numerics/Vector.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Numerics/Vector.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Geometry/Grid3D.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Geometry/Grid3D.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Geometry/GridUtils.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Geometry/GridUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Geometry/point.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Geometry/point.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Geometry/Transform.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Geometry/Transform.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Geometry/Transform2D.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Geometry/Transform2D.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Geometry/Transform3D.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Geometry/Transform3D.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Geometry/UniformGrid3D.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Geometry/UniformGrid3D.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Geometry/UniformRealValueGrid3D.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Geometry/UniformRealValueGrid3D.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Geometry/Utils.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Geometry/Utils.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Features/Feature.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/Features/Feature.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/ChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/ChemicalFeature.h... Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/FreeChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202409.6/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... Searc/build/reproducible-path/rdkit-202409.6/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-202409.6/Code/GraphMol/MolOps.h:1187: warning: documented symbol 'modifies molecule in RDKit::MolOps::place' was not declared or defined. /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolOps.h:1203: warning: documented symbol 'modifies molecule in RDKit::MolOps::place' was not declared or defined. /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Pipeline.h:90: warning: documented symbol 'enum RDKIT_MOLSTANDARDIZE_EXPORT RDKit::MolStandardize::PipelineStatus' was not declared or defined. /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupUtils.h:94: 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 82 of file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupUtils.h 'RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(const RGroupRows &rgr, const std::string &prefix="")' at line 86 of file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupUtils.h 'RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(const RGroupColumn &rgr, const std::string &prefix="")' at line 90 of file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupUtils.h /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:132: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:206: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:84: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:139: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:213: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:87: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:142: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:216: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:135: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:209: warning: Found unknown command '\override' hing 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 RealValueVect.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 ChiralViolationContribs.h... Generating code for file DistGeomUtils.h... Generating code for file DistViolationContrib.h... Generating code for file DistViolationContribs.h... Generating code for file FourthDimContrib.h... Generating code for file FourthDimContribs.h... Generating code for file TriangleSmooth.h... Generating code for file Feature.h... Generating code for file AngleConstraints.h... Generating code for file Contrib.h... Generating code for file DistanceConstraints.h... Generating code for file ForceField.h... Generating code for file OopBend.h... Generating code for file StretchBend.h... Generating code for file AngleBend.h... Generating code for file AngleBend.h... Generating code for file AngleConstraint.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 DistanceConstraint.h... Generating code for file Inversion.h... Generating code for file Inversions.h... Generating code for file Nonbonded.h... Generating code for file Nonbonded.h... Generating code for file Params.h... Generating code for file Params.h... Generating code for file PositionConstraint.h... Generating code for file PositionConstraint.h... Generating code for file PositionConstraint.h... Generating code for file TorsionAngle.h... Generating code for file TorsionAngle.h... Generating code for file TorsionConstraint.h... Generating code for file TorsionConstraint.h... Generating code for file TorsionConstraint.h... Generating code for file Utils.h... Generating code for file Utils.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 UniformRealValueGrid3D.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 Atropisomers.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 AtropisomerBond.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 DCLV.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 FileWriters.h... Generating code for file GeneralFileReader.h... Generating code for file MaestroProperties.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 MolSupplier.v1API.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 TorsionAngleContribs.h... Generating code for file TorsionAngleM6.h... Generating code for file TorsionPreferences.h... Generating code for file FFConvenience.h... Generating code for file MMFF.h... Generating code for file AtomTyper.h... Generating code for file AtomTyper.h... Generating code for file Builder.h... Generating code for file Builder.h... Generating code for file 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 MIFDescriptors.h... Generating code for file MolInterchange.h... Generating code for file MolOps.h... Generating code for file MolPickler.h... Generating code for file MolProcessing.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 Pipeline.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 CanonicalizeStereoGroups.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 Tautomer.h... Generating code for file Tautomer.h... Generating code for file Utilites.h... Generating code for file Subgraphs.h... Generating code for file SubgraphUtils.h... 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 SearchResults.h... Generating code for file Synthon.h... Generating code for file SynthonSet.h... Generating code for file SynthonSpace.h... Generating code for file SynthonSpaceFingerprintSearcher.h... Generating code for file SynthonSpaceSearch_details.h... Generating code for file SynthonSpaceSearcher.h... Generating code for file SynthonSpaceSubstructureSearcher.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 ControlCHandler.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 CatalogE/build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitOps.h:188: warning: found at different nesting level (7) than expected (4) /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitOps.h:189: warning: end of comment block while expecting command ntry.h... Generating docs for file CatalogParams.h... Generating docs for file ChemicalFeature.h... Generating docs for file FreeChemicalFeature.h... Generating docs for file MetricFuncs.h... Generating docs for file MetricMatrixCalc.h... Generating docs for file base64.h... Generating docs for file BitOps.h... Generating docs for file BitVect.h... Generating docs for file BitVects.h... Generating docs for file BitVectUtils.h... Generating docs for file DatastructsException.h... Generating docs for file DatastructsStreamOps.h... Generating docs for file DiscreteDistMat.h... Generating docs for file DiscreteValueVect.h... Generating docs for file ExplicitBitVect.h... Generating docs for file FPBReader.h... Generating docs for file MultiFPBReader.h... Generating docs for file RealValueVect.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 ChiralViolationContribs.h... Generating docs for file DistGeomUtils.h... Generating docs for file DistViolationContrib.h... Generating docs for file DistViolationContribs.h... Generating docs for file FourthDimContrib.h... Generating docs for file FourthDimContribs.h... Generating docs for file TriangleSmooth.h... Generating docs for file Feature.h... Generating docs for file AngleConstraints.h... Generating docs for file Contrib.h... Generating docs for file DistanceConstraints.h... Generating docs for file ForceField.h... Generating docs for file OopBend.h... Generating docs for file StretchBend.h... Generating docs for file AngleBend.h... Generating docs for file AngleBend.h... Generating docs for file AngleConstraint.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 DistanceConstraint.h... Generating docs for file Inversion.h... Generating docs for file Inversions.h... Generating docs for file Nonbonded.h... Generating docs for file Nonbonded.h... Generating docs for file Params.h... Generating docs for file Params.h... Generating docs for file PositionConstraint.h... Generating docs for file PositionConstraint.h... Generating docs for file PositionConstraint.h... Generating docs for file TorsionAngle.h... Generating docs for file TorsionAngle.h... Generating docs for file TorsionConstraint.h... Generating docs for file TorsionConstraint.h... Generating docs for file TorsionConstraint.h... Generating docs for file Utils.h... Generating docs for file Utils.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 UniformRealValueGrid3D.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 Atropisomers.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 AtropisomerBond.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 DCLV.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... 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Generating docs for file MolP/build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery' rocessing.h... Generating docs for file AcidBaseCatalogEntry.h... Generating docs for file AcidBaseCatalogParams.h... Generating docs for file AcidBaseCatalogUtils.h... Generating docs for file Charge.h... Generating docs for file Fragment.h... Generating docs for file FragmentCatalogEntry.h... Generating docs for file FragmentCatalogParams.h... Generating docs for file FragmentCatalogUtils.h... Generating docs for file Metal.h... Generating docs for file MolStandardize.h... Generating docs for file Normalize.h... Generating docs for file Pipeline.h... Generating docs for file TautomerCatalogEntry.h... Generating docs for file TautomerCatalogParams.h... Generating docs for file TautomerCatalogUtils.h... 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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... G/build/reproducible-path/rdkit-202409.6/Code/DistGeom/DistGeomUtils.h:93: 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-202409.6/Code/DistGeom/ChiralViolationContribs.h:46: warning: argument 'cset' of command @param is not found in the argument list of DistGeom::ChiralViolationContribs::ChiralViolationContribs(ForceFields::ForceField *owner) /build/reproducible-path/rdkit-202409.6/Code/DistGeom/ChiralViolationContribs.h:46: warning: argument 'weight' of command @param is not found in the argument list of DistGeom::ChiralViolationContribs::ChiralViolationContribs(ForceFields::ForceField *owner) /build/reproducible-path/rdkit-202409.6/Code/DistGeom/FourthDimContribs.h:36: warning: argument 'idx' of command @param is not found in the argument list of DistGeom::FourthDimContribs::FourthDimContribs(ForceFields::ForceField *owner) /build/reproducible-path/rdkit-202409.6/Code/DistGeom/FourthDimContribs.h:36: warning: argument 'weight' of command @param is not found in the argument list of DistGeom::FourthDimContribs::FourthDimContribs(ForceFields::ForceField *owner) /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraint.h:24: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraint.h:24: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraint.h:24: warning: The following parameters of ForceFields::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-202409.6/Code/ForceField/AngleConstraints.h:65: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, bool relative, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraints.h:65: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, bool relative, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraints.h:65: warning: The following parameters of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, bool relative, double minAngleDeg, double maxAngleDeg, double forceConst) are not documented: parameter 'minAngleDeg' parameter 'maxAngleDeg' /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraints.h:53: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraints.h:53: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraints.h:53: warning: The following parameters of ForceFields::AngleConstraintContribs::addContrib(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-202409.6/Code/ForceField/DistanceConstraints.h:61: warning: argument 'forceConst' of command @param is not found in the argument list of ForceFields::DistanceConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, bool relative, double minLen, double maxLen, double forceConstant) /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraints.h:61: warning: The following parameter of ForceFields::DistanceConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, bool relative, double minLen, double maxLen, double forceConstant) is not documented: parameter 'forceConstant' /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraints.h:50: warning: argument 'forceConst' of command @param is not found in the argument list of ForceFields::DistanceConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, double minLen, double maxLen, double forceConstant) /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraints.h:50: warning: The following parameter of ForceFields::DistanceConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, double minLen, double maxLen, double forceConstant) is not documented: parameter 'forceConstant' /build/reproducible-path/rdkit-202409.6/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-202409.6/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-202409.6/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-202409.6/Code/ForceField/PositionConstraint.h:25: warning: argument 'minDispl' of command @param is not found in the argument list of ForceFields::PositionConstraintContrib::PositionConstraintContrib(ForceField *owner, unsigned int idx, double maxDispl, double forceConst) /build/reproducible-path/rdkit-202409.6/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-202409.6/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-202409.6/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-202409.6/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-202409.6/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-202409.6/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-202409.6/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 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::ChiralViolationContribs... Generating docs for compound DistGeom::ChiralViolationContribsParams... Generating docs for compound DistGeom::DistViolationContrib... Generating docs for compound DistGeom::DistViolationContribs... Generating docs for compound DistGeom::DistViolationContribsParams... Generating docs for compound DistGeom::FourthDimContrib... Generating docs for compound DistGeom::FourthDimContribs... Generating docs for compound DistGeom::FourthDimContribsParams... Generating docs for namespace ForceFields Generating docs for compound ForceFields::AngleConstraintContrib... Generating docs for compound ForceFields::AngleConstraintContribs... Generating docs for compound ForceFields::AngleConstraintContribsParams... Generating docs for compound ForceFields::DistanceConstraintContrib... Generating docs for compound ForceFields::DistanceConstraintContribs... Generating docs for compound ForceFields::DistanceConstraintContribsParams... Generating docs for compound ForceFields::ForceField... Generating docs for compound ForceFields::ForceFieldContrib... Generating docs for compound ForceFields::PositionConstraintContrib... Generating docs for compound ForceFields::TorsionConstraintContrib... 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 compound ForceFields::CrystalFF::TorsionAngleContribs... Generating docs for compound ForceFields::CrystalFF::TorsionAngleContribsParams... Generating docs for namespace ForceFields::MMFF Generating docs for compound ForceFields::MMFF::AngleBendContrib... Generating docs for compound ForceFields::MMFF::BondStretchContrib... Generating docs for compound ForceFields::MMFF::EleContrib... Generating docs for compound ForceFields::MMFF::MMFFAngle... Generating docs for compound ForceFields::MMFF::MMFFAngleCollection... Generating docs for compound ForceFields::MMFF::MMFFAromCollection... Generating docs for compound ForceFields::MMFF::MMFFBndkCollection... Generating docs for compound ForceFields::MMFF::MMFFBond... Generating docs for compound ForceFields::MMFF::MMFFBondCollection... Generating docs for compound ForceFields::MMFF::MMFFChg... Generating docs for compound ForceFields::MMFF::MMFFChgCollection... Generating docs for compound ForceFields::MMFF::MMFFCovRadPauEle... Generating docs for compound ForceFields::MMFF::MMFFCovRadPauEleCollection... Generating docs for compound ForceFields::MMFF::MMFFDef... Generating docs for compound ForceFields::MMFF::MMFFDefCollection... Generating docs for compound ForceFields::MMFF::MMFFDfsbCollection... 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... Gener/build/reproducible-path/rdkit-202409.6/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-202409.6/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-202409.6/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-202409.6/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-202409.6/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-202409.6/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-202409.6/Code/GraphMol/Depictor/RDDepictor.h:392: 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-202409.6/Code/GraphMol/Depictor/RDDepictor.h:392: 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' ating 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::StretchBendContrib... Generating docs for compound ForceFields::MMFF::TorsionAngleContrib... 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::AtomicParams... Generating docs for compound ForceFields::UFF::BondStretchContrib... Generating docs for compound ForceFields::UFF::InversionContrib... Generating docs for compound ForceFields::UFF::InversionContribs... Generating docs for compound ForceFields::UFF::InversionContribsParams... Generating docs for compound ForceFields::UFF::ParamCollection... Generating docs for compound ForceFields::UFF::TorsionAngleContrib... Generating docs for compound ForceFields::UFF::UFFAngle... Generating docs for compound ForceFields::UFF::UFFBond... Generating docs for compound ForceFields::UFF::UFFInv... Generating docs for compound ForceFields::UFF::UFFTor... Generating docs for compound ForceFields::UFF::UFFVdW... Generating docs for compound ForceFields::UFF::vdWContrib... Generating docs for namespace ForceFields::UFF::Params Generating docs for namespace ForceFields::UFF::Utils Generating docs for namespace Invar Generating docs for compound Invar::Invariant... Generating docs for namespace MolTransforms Generating docs for namespace Queries Generating docs for compound Queries::AndQuery... Generating docs for compound Queries::EqualityQuery... Generating docs for compound Queries::GreaterEqualQuery... Generating docs for compound Queries::GreaterQuery... Generating docs for compound Queries::Int2Type... Generating docs for compound Queries::LessEqualQuery... Generating docs for compound Queries::LessQuery... Generating docs for compound Queries::OrQuery... Generating docs for compound Queries::Query... Generating docs for compound Queries::RangeQuery... Generating docs for compound Queries::SetQuery... Generating docs for compound Queries::XOrQuery... Generating docs for namespace Rankers Generating docs for namespace RDCatalog Generating docs for compound RDCatalog::Catalog... Generating docs for compound RDCatalog::CatalogEntry... Generating docs for compound RDCatalog::CatalogParams... Generating docs for compound RDCatalog::HierarchCatalog... Generating docs for nested compound RDCatalog::HierarchCatalog::vertex_entry_t... Generating docs for namespace RDDataManip Generating docs for compound RDDataManip::MetricMatrixCalc... Generating docs for namespace RDDepict Generating docs for compound RDDepict::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 compound RDGeom::UniformRealValueGrid3D... Generating docs for namespace RDInfoTheory Generating docs for compound RDInfoTheory::BitCorrMatGenerator... Generating docs for compound RDInfoThe/build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstanceGroup.h:276: warning: The following parameter of RDKit::addSubstanceGroup(ROMol &mol, SubstanceGroup sgroup) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202409.6/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-202409.6/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-202409.6/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-202409.6/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmilesWrite.h:232: 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-202409.6/Code/GraphMol/FileParsers/FileWriters.h:36: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToMolBlock(const ROMol &mol, const MolWriterParams ¶ms, int confId=-1) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:36: warning: The following parameter of RDKit::MolToMolBlock(const ROMol &mol, const MolWriterParams ¶ms, int confId=-1) is not documented: parameter 'params' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:111: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToMolFile(const ROMol &mol, const std::string &fName, const MolWriterParams ¶ms, int confId=-1) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:111: warning: The following parameter of RDKit::MolToMolFile(const ROMol &mol, const std::string &fName, const MolWriterParams ¶ms, int confId=-1) is not documented: parameter 'params' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinParser.h:180: warning: The following parameters of RDKit::MolToMrvBlock(const ROMol &mol, bool includeStereo=true, int confId=-1, bool kekulize=true, bool prettyPrint=false) are not documented: parameter 'mol' parameter 'includeStereo' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinParser.h:155: warning: The following parameters of RDKit::MolToMrvFile(const ROMol &mol, const std::string &fName, bool includeStereo=true, int confId=-1, bool kekulize=true, bool prettyPrint=false) are not documented: parameter 'mol' parameter 'fName' parameter 'includeStereo' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:227: 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-202409.6/Code/GraphMol/FileParsers/FileWriters.h:227: 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-202409.6/Code/GraphMol/FileParsers/FileWriters.h:97: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToV2KMolBlock(const ROMol &mol, const MolWriterParams ¶ms=MolWriterParams(), int confId=-1) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:97: warning: The following parameter of RDKit::MolToV2KMolBlock(const ROMol &mol, const MolWriterParams ¶ms=MolWriterParams(), int confId=-1) is not documented: parameter 'params' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:66: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToV3KMolBlock(const ROMol &mol, const MolWriterParams ¶ms, int confId=-1) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:66: warning: The following parameter of RDKit::MolToV3KMolBlock(const ROMol &mol, const MolWriterParams ¶ms, int confId=-1) is not documented: parameter 'params' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:142: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToV3KMolFile(const ROMol &mol, const std::string &fName, const MolWriterParams ¶ms, int confId=-1) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:142: warning: The following parameter of RDKit::MolToV3KMolFile(const ROMol &mol, const std::string &fName, const MolWriterParams ¶ms, int confId=-1) is not documented: parameter 'params' /build/reproducible-path/rdkit-202409.6/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-202409.6/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-202409.6/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-202409.6/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-202409.6/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-202409.6/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-202409.6/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-202409.6/Code/GraphMol/Substruct/SubstructMatch.h:84: 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-202409.6/Code/GraphMol/Substruct/SubstructMatch.h:84: 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-202409.6/Code/GraphMol/Substruct/SubstructMatch.h:97: 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-202409.6/Code/GraphMol/Substruct/SubstructMatch.h:97: 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-202409.6/Code/GraphMol/Substruct/SubstructMatch.h:152: 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-202409.6/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-202409.6/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-202409.6/Code/GraphMol/ChemReactions/Reaction.h:219: warning: The following parameter of RDKit::ChemicalReaction::runReactants(const MOL_SPTR_VECT reactants, unsigned int numProducts=1000) const is not documented: parameter 'numProducts' /build/reproducible-path/rdkit-202409.6/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 98 in file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: 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-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: 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-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::FilterMatcherBase::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const=0 is not documented: parameter 'matchVect' ory::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::ControlCHandler... Generating docs for compound RDKit::CustomPropHandler... Generating docs for compound RDKit::CXXAtomIterator... Generating docs for nested compound RDKit::CXXAtomIterator::CXXAtomIter... Generating docs for compound RDKit::CXXBondIterator... Generating docs for nested compound RDKit::CXXBondIterator::CXXBondIter... Generating docs for compound RDKit::DataStructsExplicitBitVecPropHandler... Generating docs for compound RDKit::Dict... Generating docs for nested compound RDKit::Dict::Pair... Generating docs for compound RDKit::DiscreteDistMat... Generating docs for compound RDKit::DiscreteValueVect... Generating docs for compound RDKit::DrawColour... Generating docs for compound RDKit::EnumerateLibrary... Generating docs for compound RDKit::EnumerateLibraryBase... Generating docs for compound RDKit::EnumerationParams... Generating docs for compound RDKit::EnumerationStrategyBase... Generating docs for compound RDKit::EnumerationStrategyException... Generating docs for compound RDKit::EvenSamplePairsStrategy... Generating docs for compound RDKit::ExclusionList... Generating docs for compound RDKit::FeatureFileParseException... Generating docs for compound RDKit::FileParseException... Generating docs for compound RDKit::FilterCatalog... Generating docs for compound RDKit::FilterCatalogEntry... Generating docs for compound RDKit::FilterCatalogParams... Generating docs for compound 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::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 RD/build/reproducible-path/rdkit-202409.6/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-202409.6/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-202409.6/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-202409.6/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-202409.6/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-202409.6/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-202409.6/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' Kit::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::HasPropWithValueQueryBase... 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::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::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::MolWriter... Generating docs for compound RDKit::MolWriterParams... Generating docs for compound RDKit::MolzipParams... Generating docs for compound RDKit::MrvWriterParams... Generating docs for compound RDKit::MultiFPBReader... Generating docs for compound RDKit::PairHolder... Generating docs for compound RDKit::PatternHolder... 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 c/build/reproducible-path/rdkit-202409.6/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-202409.6/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 98 in file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::SmartsMatcher::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202409.6/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-202409.6/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-202409.6/Code/GraphMol/Fingerprints/AtomPairs.h:97: 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-202409.6/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-202409.6/Code/GraphMol/Canon.h:98: 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' ompound 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::RealValueVect... 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::RigorousEnhancedStereoException... 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::SDWriter... Generating docs for compound RDKit::SLNParseException... Generating docs for compound RDKit::SmartsMatcher... Generating docs for compound RDKit::SmilesWriteParams... Generating docs for compound RDKit::SmilesWriter... Generating docs for compound RDKit::Snapshot... Generating docs for compound RDKit::SparseIntVect... Generating docs for compound RDKit::StereoBondThresholds... Generating docs for compound RDKit::StereoGroup... Generating docs for compound RDKit::SubstanceGroup... Generating docs for nested compound RDKit::SubstanceGroup::AttachPoint... Generating docs for nested compound RDKit::SubstanceGroup::CState... Generating docs for compound RDKit::SubstanceGroupException... Generating docs for compound RDKit::SubstructLibrary... Generating docs for compound RDKit::SubstructMatchParameters... Generating docs for compound RDKit::TautomerPatternHolder... Generating docs for compound RDKit::TautomerQuery... Generating docs for compound RDKit::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::Atropisomers 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... Generat/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Chirality.h:414: warning: The following parameters of RDKit::Chirality::findMesoCenters(const ROMol &mol, bool includeIsotopes=true, bool includeAtomMaps=false) are not documented: parameter 'includeIsotopes' parameter 'includeAtomMaps' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Chirality.h:143: warning: The following parameter of RDKit::Chirality::findPotentialStereo(ROMol &mol, bool cleanIt, bool flagPossible=true) is not documented: parameter 'flagPossible' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Chirality.h:195: warning: The following parameter of RDKit::Chirality::getTrigonalBipyramidalAxialBond(const Atom *center, int which=0) is not documented: parameter 'center' /build/reproducible-path/rdkit-202409.6/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-202409.6/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-202409.6/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-202409.6/Code/GraphMol/Descriptors/USRDescriptor.h:68: warning: The following parameter of RDKit::Descriptors::USRCAT(const ROMol &mol, std::vector< double > &descriptor, std::vector< std::vector< unsigned int > > &atomIds, int confId=-1) is not documented: parameter 'atomIds' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/Embedder.h:328: warning: The following parameter of RDKit::DGeomHelpers::EmbedMultipleConfs(ROMol &mol, INT_VECT &res, unsigned int numConfs=10, int numThreads=1, unsigned int maxIterations=30, int seed=-1, bool clearConfs=true, bool useRandomCoords=false, double boxSizeMult=2.0, bool randNegEig=true, unsigned int numZeroFail=1, double pruneRmsThresh=-1.0, const std::map< int, RDGeom::Point3D > *coordMap=nullptr, double optimizerForceTol=1e-3, bool ignoreSmoothingFailures=false, bool enforceChirality=true, bool useExpTorsionAnglePrefs=false, bool useBasicKnowledge=false, bool verbose=false, double basinThresh=5.0, bool onlyHeavyAtomsForRMS=false, unsigned int ETversion=2, bool useSmallRingTorsions=false, bool useMacrocycleTorsions=true, bool useMacrocycle14config=true, unsigned int timeout=0) is not documented: parameter 'timeout' /build/reproducible-path/rdkit-202409.6/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-202409.6/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 98 in file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: 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-202409.6/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 98 in file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: 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-202409.6/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 98 in file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::FilterMatchOps::Or::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' ing 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 compound RDKit::Chirality::WedgeInfoAtropisomer... Generating docs for compound RDKit::Chirality::WedgeInfoBase... Generating docs for compound RDKit::Chirality::WedgeInfoChiral... Generating docs for namespace RDKit::Chirality::detail Generating docs for namespace RDKit::CIPLabeler Generating docs for compound RDKit::CIPLabeler::AtropisomerBond... 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... Generating docs for compound RDKit::Descriptors::CrippenParams... Generating docs for compound RDKit::Descriptors::DoubleCubicLatticeVolume... 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::FileParsers Generating docs for namespace RDKit::FileParsers::schrodinger 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 do/build/reproducible-path/rdkit-202409.6/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-202409.6/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-202409.6/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-202409.6/Code/GraphMol/MMPA/MMPA.h:28: 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-202409.6/Code/GraphMol/MMPA/MMPA.h:49: 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-202409.6/Code/GraphMol/MolAlign/AlignMolecules.h:149: 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-202409.6/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-202409.6/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-202409.6/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-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCH.h:28: warning: The following parameter of RDKit::MolDraw2D_detail::DrawMolMCH::DrawMolMCH(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) is not documented: parameter 'highlight_radii' /build/reproducible-path/rdkit-202409.6/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-202409.6/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-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h:36: 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-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h:36: 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' cs 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::MMPA::detail 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::MolAlign::details 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::DrawMolMCHCircleAndLine... 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::DrawTextFTSV/build/reproducible-path/rdkit-202409.6/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-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:132: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:135: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:139: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:142: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:142: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:132: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:139: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:135: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:84: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:87: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:87: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:84: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:206: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:209: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:213: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:216: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:216: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:206: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:213: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:209: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.6/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-202409.6/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-202409.6/Code/GraphMol/MolOps.h:330: warning: The following parameters of RDKit::MolOps::mergeQueryHs(const ROMol &mol, bool mergeUnmappedOnly=false, bool mergeIsotopes=false) are not documented: parameter 'mergeUnmappedOnly' parameter 'mergeIsotopes' G... 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::LinePair... 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::Hybridizations... Generating docs for compound RDKit::MolOps::RemoveHsParameters... Generating docs for namespace RDKit::MolOps::details Generating docs for namespace RDKit::MolProcessing Generating docs for namespace RDKit::MolProcessing::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::CompositeValidation... Generating docs for compound RDKit::MolStandardize::DisallowedAtomsValidation... Generating docs for compound RDKit::MolStandardize::DisallowedRadicalValidation... Generating docs for compound RDKit::MolStandardize::FeaturesValidation... 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::Is2DValidation... 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::Layout2DValidation... Generating docs for compound RDKit::MolStandardize::MetalDisconnector... Generating docs for compound RDKit::MolStandardize::MetalDisconnectorOptions... Generating docs for compound RDKit::MolStandardize::MolVSValidation... 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::Pipeline... Generating docs for compound RDKit::MolStandardize::PipelineLogEntry... Generating docs for compound RDKit::MolStandardize::PipelineOptions... Generating docs for compound RDKit::MolStandardize::PipelineResult... Generating docs /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.h:208: warning: argument 'countSimulation' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.h:208: warning: argument 'includeChirality' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.h:208: warning: argument 'onlyNonzeroInvariants' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.h:273: warning: argument 'countSimulation' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.h:273: warning: argument 'includeChirality' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.h:273: warning: argument 'onlyNonzeroInvariants' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202409.6/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-202409.6/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-202409.6/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-202409.6/Code/GraphMol/ReducedGraphs/ReducedGraphs.h:26: warning: The following parameter of RDKit::ReducedGraphs::generateMolExtendedReducedGraph(const ROMol &mol, std::vector< boost::dynamic_bitset<> > *atomTypes=nullptr) is not documented: parameter 'atomTypes' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmilesWrite.h:104: warning: argument 'bondIn' of command @param is not found in the argument list of RDKit::SmilesWrite::GetAtomSmiles(const Atom *atom, bool doKekule=false, const Bond *=nullptr, bool allHsExplicit=false, bool isomericSmiles=true) for compound RDKit::MolStandardize::RDKitValidation... Generating docs for compound RDKit::MolStandardize::Reionizer... Generating docs for compound RDKit::MolStandardize::StereoValidation... 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::ValidationMethod... Generating docs for namespace RDKit::MolStandardize::defaults Generating docs for namespace RDKit::MolStandardize::Operations Generating docs for namespace RDKit::MolStandardize::TautomerScoringFunctions Generating docs for compound RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm... 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 RDKit::SLNParse::AttribType... Generating docs for namespace RDKit::SmartsWrite Generating docs for namespace RDKit::SmilesParse Generating docs for compound RDKit::SmilesParse::SmilesParseException... Generating docs for namespace RDKit::SmilesWrite Generating /build/reproducible-path/rdkit-202409.6/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-202409.6/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-202409.6/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=false, const uint32_t torsionAtomCount=4, const bool countSimulation=true, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const std::uint32_t fpSize=2048) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:32: warning: The following parameter of RDKit::TopologicalTorsion::TopologicalTorsionArguments::TopologicalTorsionArguments(const bool includeChirality=false, const uint32_t torsionAtomCount=4, const bool countSimulation=true, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const std::uint32_t fpSize=2048) is not documented: parameter 'countSimulation' /build/reproducible-path/rdkit-202409.6/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-202409.6/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-202409.6/Code/GraphMol/FileParsers/CDXMLParser.h:95: warning: argument 'fileName' of command @param is not found in the argument list of RDKit::v1::CDXMLFileToMols(const std::string &filename, bool sanitize=true, bool removeHs=true) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/CDXMLParser.h:95: warning: The following parameter of RDKit::v1::CDXMLFileToMols(const std::string &filename, bool sanitize=true, bool removeHs=true) is not documented: parameter 'filename' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileParsers.h:76: warning: argument 'line' from the argument list of RDKit::v1::MolDataStreamToMol has multiple @param documentation sections /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/CDXMLParser.h:46: warning: argument 'fileName' of command @param is not found in the argument list of RDKit::v2::CDXMLParser::MolsFromCDXMLFile(const std::string &filename, const CDXMLParserParams ¶ms=CDXMLParserParams()) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/CDXMLParser.h:46: warning: The following parameter of RDKit::v2::CDXMLParser::MolsFromCDXMLFile(const std::string &filename, const CDXMLParserParams ¶ms=CDXMLParserParams()) is not documented: parameter 'filename' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:176: warning: argument 'sanitize' of command @param is not found in the argument list of RDKit::v2::FileParsers::SDMolSupplier::SDMolSupplier(const std::string &fileName, const MolFileParserParams ¶ms=MolFileParserParams()) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:176: warning: argument 'removeHs' of command @param is not found in the argument list of RDKit::v2::FileParsers::SDMolSupplier::SDMolSupplier(const std::string &fileName, const MolFileParserParams ¶ms=MolFileParserParams()) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:176: warning: argument 'strictParsing' of command @param is not found in the argument list of RDKit::v2::FileParsers::SDMolSupplier::SDMolSupplier(const std::string &fileName, const MolFileParserParams ¶ms=MolFileParserParams()) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:176: warning: The following parameter of RDKit::v2::FileParsers::SDMolSupplier::SDMolSupplier(const std::string &fileName, const MolFileParserParams ¶ms=MolFileParserParams()) is not documented: parameter 'params' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'delimiter' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams()) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'smilesColumn' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams()) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'nameColumn' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams()) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'titleLine' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams()) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'sanitize' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams()) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: The following parameter of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams()) is not documented: parameter 'params' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: argument 'nameRecord' of command @param is not found in the argument list of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams()) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: argument 'confId2D' of command @param is not found in the argument list of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams()) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: argument 'confId3D' of command @param is not found in the argument list of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams()) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: argument 'sanitize' of command @param is not found in the argument list of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams()) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: The following parameter of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams()) is not documented: parameter 'params' 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::SynthonSpaceSearch Generating docs for compound RDKit::SynthonSpaceSearch::SearchResults... Generating docs for compound RDKit::SynthonSpaceSearch::Synthon... Generating docs for compound RDKit::SynthonSpaceSearch::SynthonSet... Generating docs for compound RDKit::SynthonSpaceSearch::SynthonSpace... Generating docs for compound RDKit::SynthonSpaceSearch::SynthonSpaceFingerprintSearcher... Generating docs for compound RDKit::SynthonSpaceSearch::SynthonSpaceHitSet... Generating docs for compound RDKit::SynthonSpaceSearch::SynthonSpaceSearcher... Generating docs for compound RDKit::SynthonSpaceSearch::SynthonSpaceSearchParams... Generating docs for compound RDKit::SynthonSpaceSearch::SynthonSpaceSubstructureSearcher... Generating docs for namespace RDKit::SynthonSpaceSearch::details Generating docs for compound RDKit::SynthonSpaceSearch::details::Stepper... 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 RDKit::v1 Generating docs for compound RDKit::v1::ForwardSDMolSupplier... Generating docs for compound RDKit::v1::MolSupplier... Generating docs for compound RDKit::v1::SDMolSupplier... Generating docs for compound RDKit::v1::SmartsParserParams... Generating docs for compound RDKit::v1::SmilesMolSupplier... Generating docs for compound RDKit::v1::SmilesParserParams... Generating docs for compound RDKit::v1::TDTMolSupplier... Generating docs for namespace RDKit::v2 Generating docs for namespace RDKit::v2::CDXMLParser Generating docs for compound RDKit::v2::CDXMLParser::CDXMLParserParams... Generating docs for namespace RDKit::v2::FileParsers Generating docs for compound RDKit::v2::FileParsers::ForwardSDMolSupplier... Generating docs for compound RDKit::v2::FileParsers::Mol2ParserParams... Generating docs for compound RDKit::v2::FileParsers::MolFileParserParams... Generating docs for compound RDKit::v2::FileParsers::MolFileUnhandledFeatureException... Generating docs for compound RDKit::v2::FileParsers::MolSupplier... Generating docs for compound RDKit::v2::FileParsers::PDBParserParams... Generating docs for compound RDKit::v2::FileParsers::SDMolSupplier... Generating docs for compound RDKit::v2::FileParsers::SmilesMolSupplier... Generating docs for compound RDKit::v2::FileParsers::SmilesMolSupplierParams... Generating docs for compound RDKit::v2::FileParsers::TDTMolSupplier... Generating docs for compound RDKit::v2::FileParsers::TDTMolSupplierParams... Generating docs for compound RDKit::v2::FileParsers::TPLParserParams... Generating docs for namespace RDKit::v2::MarvinParser Generating docs for compound RDKit::v2::MarvinParser::MrvParserParams... Generating docs for namespace RD/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/MIFDescriptors.h:117: warning: argument 'pos' of command @param is not found in the argument list of RDMIF::Coulomb::Coulomb(const std::vector< double > &charges, const std::vector< RDGeom::Point3D > &positions, double probeCharge=1.0, bool absVal=false, double alpha=0.0, double cutoff=1.0) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/MIFDescriptors.h:117: warning: The following parameter of RDMIF::Coulomb::Coulomb(const std::vector< double > &charges, const std::vector< RDGeom::Point3D > &positions, double probeCharge=1.0, bool absVal=false, double alpha=0.0, double cutoff=1.0) is not documented: parameter 'positions' /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/MIFDescriptors.h:220: warning: argument 'pos' of command @param is not found in the argument list of RDMIF::CoulombDielectric::CoulombDielectric(const std::vector< double > &charges, const std::vector< RDGeom::Point3D > &positions, double probeCharge=1.0, bool absVal=false, double alpha=0.0, double cutoff=1.0, double epsilon=80.0, double xi=4.0) /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/MIFDescriptors.h:220: warning: The following parameter of RDMIF::CoulombDielectric::CoulombDielectric(const std::vector< double > &charges, const std::vector< RDGeom::Point3D > &positions, double probeCharge=1.0, bool absVal=false, double alpha=0.0, double cutoff=1.0, double epsilon=80.0, double xi=4.0) is not documented: parameter 'positions' /build/reproducible-path/rdkit-202409.6/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-202409.6/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-202409.6/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-202409.6/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-202409.6/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-202409.6/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 Kit::v2::ReactionParser Generating docs for namespace RDKit::v2::SmilesParse Generating docs for namespace RDLog Generating docs for namespace RDMIF Generating docs for compound RDMIF::Coulomb... Generating docs for compound RDMIF::CoulombDielectric... Generating docs for compound RDMIF::HBond... Generating docs for compound RDMIF::Hydrophilic... Generating docs for compound RDMIF::MMFFVdWaals... Generating docs for compound RDMIF::UFFVdWaals... Generating docs for compound RDMIF::VdWaals... 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 36956/65536 hits=217530 misses=41055 symbol lookup cache used 32486/65536 hits=291606 misses=32486 finished... (cd /build/reproducible-path/rdkit-202409.6/Docs/Book; RDBASE=/build/reproducible-path/rdkit-202409.6 /usr/bin/make html) make[2]: Entering directory '/build/reproducible-path/rdkit-202409.6/Docs/Book' mkdir -p _build/html/cppapi cp -r /build/reproducible-path/rdkit-202409.6/Code/docs/* _build/html/cppapi cp -r C++Examples _build/html/ sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v8.1.3 loading translations [en]... done WARNING: html_static_path entry '_static' does not exist myst v4.0.1: 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_sort=True, 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 262 source files that are out of date updating environment: [new config] 262 added, 0 changed, 0 removed reading sources... 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/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:850: WARNING: duplicate label drawing molecules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:1089: WARNING: duplicate label substructure searching, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:1154: WARNING: duplicate label stereochemistry in substructure matches, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:1192: WARNING: duplicate label atom map indices in smarts, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:3434: WARNING: duplicate label the sssr problem, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:3848: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/Cookbook.rst [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md:424: WARNING: duplicate label building rdkit for development, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md [autosectionlabel.GettingStartedWithContributing] /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md:430: WARNING: duplicate label where should i put my code?, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md [autosectionlabel.GettingStartedWithContributing] /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md:434: WARNING: duplicate label coding standards, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md [autosectionlabel.GettingStartedWithContributing] /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md:447: WARNING: duplicate label tests, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md [autosectionlabel.GettingStartedWithContributing] /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md:481: WARNING: duplicate label documentation, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md [autosectionlabel.GettingStartedWithContributing] /build/reproducible-path/rdkit-202409.6/Docs/Book/Install.md:430: WARNING: duplicate label recommended extras, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/Install.md [autosectionlabel.Install] /build/reproducible-path/rdkit-202409.6/Docs/Book/Install.md:474: WARNING: duplicate label testing the build (optional, but recommended), other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/Install.md [autosectionlabel.Install] /build/reproducible-path/rdkit-202409.6/Docs/Book/Install.md:479: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst [autosectionlabel.Install] /build/reproducible-path/rdkit-202409.6/Docs/Book/Overview.md:107: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/Install.md [autosectionlabel.Overview] /build/reproducible-path/rdkit-202409.6/Docs/Book/RDKit_Book.rst:179: WARNING: duplicate label aromaticity, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/RDKit_Book.rst [autosectionlabel.RDKit_Book] /build/reproducible-path/rdkit-202409.6/Docs/Book/RDKit_Book.rst:385: WARNING: duplicate label dative bonds, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/RDKit_Book.rst [autosectionlabel.RDKit_Book] /build/reproducible-path/rdkit-202409.6/Docs/Book/RDKit_Book.rst:575: WARNING: duplicate label stereochemistry, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/Cookbook.rst [autosectionlabel.RDKit_Book] /build/reproducible-path/rdkit-202409.6/Docs/Book/RDKit_Book.rst:1304: WARNING: duplicate label chemical features, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst [autosectionlabel.RDKit_Book] /build/reproducible-path/rdkit-202409.6/Docs/Book/RDKit_Book.rst:2504: WARNING: duplicate label introduction, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/Cookbook.rst [autosectionlabel.RDKit_Book] /build/reproducible-path/rdkit-202409.6/Docs/Book/RDKit_Book.rst:2602: WARNING: duplicate label rdkit fingerprints, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst [autosectionlabel.RDKit_Book] /build/reproducible-path/rdkit-202409.6/Docs/Book/RDKit_Book.rst:2768: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/Overview.md [autosectionlabel.RDKit_Book] WARNING: autodoc: failed to import module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Avalon' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Avalon.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Avalon] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Avalon.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Avalon] WARNING: autodoc: failed to import module 'Avalon.pyAvalonTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Chem] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst:28: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Avalon.rst [autosectionlabel.source/rdkit.Chem] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst:115: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Avalon.rst [autosectionlabel.source/rdkit.Chem] WARNING: autodoc: failed to import module 'Chem.AllChem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.AtomPairs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.Chem.AtomPairs] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.AtomPairs.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.Chem.AtomPairs] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Pairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Sheridan' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Torsions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.BRICS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.BuildFragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.ChemUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.AtomPairs.rst [autosectionlabel.source/rdkit.Chem.ChemUtils] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.ChemUtils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.AtomPairs.rst [autosectionlabel.source/rdkit.Chem.ChemUtils] WARNING: autodoc: failed to import module 'Chem.ChemUtils.AlignDepict' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.BulkTester' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.DescriptorUtilities' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.SDFToCSV' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.TemplateExpand' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemicalForceFields' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Crippen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Descriptors3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Draw.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.ChemUtils.rst [autosectionlabel.source/rdkit.Chem.Draw] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Draw.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.ChemUtils.rst [autosectionlabel.source/rdkit.Chem.Draw] WARNING: autodoc: failed to import module 'Chem.Draw.IPythonConsole' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.MolDrawing' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.SimilarityMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2DQt' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.EState.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Draw.rst [autosectionlabel.source/rdkit.Chem.EState] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.EState.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Draw.rst [autosectionlabel.source/rdkit.Chem.EState] WARNING: autodoc: failed to import module 'Chem.EState.AtomTypes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState.EState_VSA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState.Fingerprinter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EnumerateHeterocycles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EnumerateStereoisomers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FastSDMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatFinderCLI' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.FeatMaps.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.EState.rst [autosectionlabel.source/rdkit.Chem.FeatMaps] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.FeatMaps.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.EState.rst [autosectionlabel.source/rdkit.Chem.FeatMaps] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapParser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapPoint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Features' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Features.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.FeatMaps.rst [autosectionlabel.source/rdkit.Chem.Features] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Features.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.FeatMaps.rst [autosectionlabel.source/rdkit.Chem.Features] WARNING: autodoc: failed to import module 'Chem.Features.FeatDirUtilsRD' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Features.ShowFeats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FilterCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fingerprints.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Features.rst [autosectionlabel.source/rdkit.Chem.Fingerprints] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fingerprints.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Features.rst [autosectionlabel.source/rdkit.Chem.Fingerprints] WARNING: autodoc: failed to import module 'Chem.Fingerprints.ClusterMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.DbFpSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.FingerprintMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.MolSimilarity' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.SimilarityScreener' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fraggle' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fraggle.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fingerprints.rst [autosectionlabel.source/rdkit.Chem.Fraggle] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fraggle.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fingerprints.rst [autosectionlabel.source/rdkit.Chem.Fraggle] WARNING: autodoc: failed to import module 'Chem.Fraggle.FraggleSim' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FragmentMatcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fragments' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FunctionalGroups' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.GraphDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Graphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Lipinski' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MACCSkeys' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolDb.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fraggle.rst [autosectionlabel.source/rdkit.Chem.MolDb] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolDb.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fraggle.rst [autosectionlabel.source/rdkit.Chem.MolDb] WARNING: autodoc: failed to import module 'Chem.MolDb.FingerprintUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb.Loader' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_orig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_sa' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolKey.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolDb.rst [autosectionlabel.source/rdkit.Chem.MolKey] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolKey.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolDb.rst [autosectionlabel.source/rdkit.Chem.MolKey] WARNING: autodoc: failed to import module 'Chem.MolKey.InchiInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolKey.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolStandardize.rst:6: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolKey.rst [autosectionlabel.source/rdkit.Chem.MolStandardize] WARNING: autodoc: failed to import module 'Chem.MolStandardize.rdMolStandardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolSurf' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PandasTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PeriodicTable' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm2D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolStandardize.rst [autosectionlabel.source/rdkit.Chem.Pharm2D] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm2D.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolKey.rst [autosectionlabel.source/rdkit.Chem.Pharm2D] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Generate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Gobbi_Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Matcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.SigFactory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm3D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm2D.rst [autosectionlabel.source/rdkit.Chem.Pharm3D] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm3D.rst:14: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm2D.rst [autosectionlabel.source/rdkit.Chem.Pharm3D] WARNING: autodoc: failed to import module 'Chem.Pharm3D.EmbedLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm3D.ExcludedVolume' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm3D.Pharmacophore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PropertyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.QED' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Randomize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Recap' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.RegistrationHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SATIS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SaltRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Scaffolds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Scaffolds.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm3D.rst [autosectionlabel.source/rdkit.Chem.Scaffolds] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Scaffolds.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm3D.rst [autosectionlabel.source/rdkit.Chem.Scaffolds] WARNING: autodoc: failed to import module 'Chem.Scaffolds.MurckoScaffold' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Scaffolds.rdScaffoldNetwork' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ShowMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SimpleEnum' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Scaffolds.rst [autosectionlabel.source/rdkit.Chem.SimpleEnum] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Scaffolds.rst [autosectionlabel.source/rdkit.Chem.SimpleEnum] WARNING: autodoc: failed to import module 'Chem.SimpleEnum.Enumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SpacialScore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Subshape.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.SimpleEnum.rst [autosectionlabel.source/rdkit.Chem.Subshape] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Subshape.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.SimpleEnum.rst [autosectionlabel.source/rdkit.Chem.Subshape] WARNING: autodoc: failed to import module 'Chem.Subshape.BuilderUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeAligner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeBuilder' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeObjects' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Suppliers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Suppliers.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Subshape.rst [autosectionlabel.source/rdkit.Chem.Suppliers] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Suppliers.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Subshape.rst [autosectionlabel.source/rdkit.Chem.Suppliers] WARNING: autodoc: failed to import module 'Chem.Suppliers.DbMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Suppliers.MolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.TemplateAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.TorsionFingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.fmcs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Suppliers.rst [autosectionlabel.source/rdkit.Chem.fmcs] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.fmcs.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Suppliers.rst [autosectionlabel.source/rdkit.Chem.fmcs] WARNING: autodoc: failed to import module 'Chem.fmcs.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.inchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdAbbreviations' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdCIPLabeler' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdChemReactions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdCoordGen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDepictor' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDeprotect' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDetermineBonds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdEHTTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdFMCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdFingerprintGenerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdForceFieldHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdFreeSASA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMHFPFingerprint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMMPA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolEnumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolInterchange' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolTransforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdPartialCharges' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdRGroupDecomposition' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdSLNParse' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdShapeAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdShapeHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdSubstructLibrary' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdSynthonSpaceSearch' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdTautomerQuery' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdchem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdfiltercatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdfragcatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdinchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdmolfiles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdmolops' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdqueries' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdtrajectory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataManip' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.DataManip] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.fmcs.rst [autosectionlabel.source/rdkit.DataManip] WARNING: autodoc: failed to import module 'DataManip.Metric' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.Metric.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.fmcs.rst [autosectionlabel.source/rdkit.DataManip.Metric] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.Metric.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.rst [autosectionlabel.source/rdkit.DataManip.Metric] WARNING: autodoc: failed to import module 'DataManip.Metric.rdMetricMatrixCalc' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataStructs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.Metric.rst [autosectionlabel.source/rdkit.DataStructs] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataStructs.rst:18: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.Metric.rst [autosectionlabel.source/rdkit.DataStructs] WARNING: autodoc: failed to import module 'DataStructs.BitEnsemble' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.BitEnsembleDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.BitUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.LazySignature' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.TopNContainer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.VectCollection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.cDataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Dbase.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataStructs.rst [autosectionlabel.source/rdkit.Dbase] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Dbase.rst:17: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataStructs.rst [autosectionlabel.source/rdkit.Dbase] WARNING: autodoc: failed to import module 'Dbase.DbConnection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbModule' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbResultSet' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.StorageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DistanceGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DistanceGeometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Dbase.rst [autosectionlabel.source/rdkit.DistanceGeometry] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DistanceGeometry.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Dbase.rst [autosectionlabel.source/rdkit.DistanceGeometry] WARNING: autodoc: failed to import module 'DistanceGeometry.DistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ForceField.rst:5: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] WARNING: autodoc: failed to import module 'ForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ForceField.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DistanceGeometry.rst [autosectionlabel.source/rdkit.ForceField] WARNING: autodoc: failed to import module 'ForceField.rdForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Geometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Geometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DistanceGeometry.rst [autosectionlabel.source/rdkit.Geometry] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Geometry.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ForceField.rst [autosectionlabel.source/rdkit.Geometry] WARNING: autodoc: failed to import module 'Geometry.rdGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.rst [autosectionlabel.source/rdkit.ML] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst:18: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Geometry.rst [autosectionlabel.source/rdkit.ML] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst:26: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Geometry.rst [autosectionlabel.source/rdkit.ML] WARNING: autodoc: failed to import module 'ML.Cluster' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Cluster.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.ML.Cluster] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Cluster.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.ML.Cluster] WARNING: autodoc: failed to import module 'ML.Cluster.Butina' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.ClusterUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.ClusterVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Clustering' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Clusters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Murtagh' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Resemblance' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Standardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Data.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Cluster.rst [autosectionlabel.source/rdkit.ML.Data] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Data.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Cluster.rst [autosectionlabel.source/rdkit.ML.Data] WARNING: autodoc: failed to import module 'ML.Data.DataUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.FindQuantBounds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.MLData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.Quantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.SplitData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.Stats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.Transforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.cQuantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Descriptors.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Data.rst [autosectionlabel.source/rdkit.ML.Descriptors] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Descriptors.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Data.rst [autosectionlabel.source/rdkit.ML.Descriptors] WARNING: autodoc: failed to import module 'ML.Descriptors.CompoundDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors.MoleculeDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors.Parser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.InfoTheory.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Descriptors.rst [autosectionlabel.source/rdkit.ML.InfoTheory] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.InfoTheory.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Descriptors.rst [autosectionlabel.source/rdkit.ML.InfoTheory] WARNING: autodoc: failed to import module 'ML.InfoTheory.BitClusterer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory.BitRank' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory.entropy' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory.rdInfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.MLUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.MLUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.InfoTheory.rst [autosectionlabel.source/rdkit.ML.MLUtils] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.MLUtils.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.InfoTheory.rst [autosectionlabel.source/rdkit.ML.MLUtils] WARNING: autodoc: failed to import module 'ML.MLUtils.VoteImg' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.MatOps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.SLT' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.SLT.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.MLUtils.rst [autosectionlabel.source/rdkit.ML.SLT] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.SLT.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.MLUtils.rst [autosectionlabel.source/rdkit.ML.SLT] WARNING: autodoc: failed to import module 'ML.SLT.Risk' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Scoring.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.SLT.rst [autosectionlabel.source/rdkit.ML.Scoring] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Scoring.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.SLT.rst [autosectionlabel.source/rdkit.ML.Scoring] WARNING: autodoc: failed to import module 'ML.Scoring.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.files' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Numerics' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Numerics.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Scoring.rst [autosectionlabel.source/rdkit.Numerics] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Numerics.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Scoring.rst [autosectionlabel.source/rdkit.Numerics] WARNING: autodoc: failed to import module 'Numerics.rdAlignment' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDConfig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDLogger' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDPaths' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDRandom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'SimDivFilters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.SimDivFilters.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Numerics.rst [autosectionlabel.source/rdkit.SimDivFilters] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.SimDivFilters.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Numerics.rst [autosectionlabel.source/rdkit.SimDivFilters] WARNING: autodoc: failed to import module 'SimDivFilters.SimilarityPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'SimDivFilters.rdSimDivPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'TestRunner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.VLib] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst:12: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.SimDivFilters.rst [autosectionlabel.source/rdkit.VLib] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst:23: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.SimDivFilters.rst [autosectionlabel.source/rdkit.VLib] WARNING: autodoc: failed to import module 'VLib.Filter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Node' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.NodeLib.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst [autosectionlabel.source/rdkit.VLib.NodeLib] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.NodeLib.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst [autosectionlabel.source/rdkit.VLib.NodeLib] WARNING: autodoc: failed to import module 'VLib.NodeLib.DbMolSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.DbPickleSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SDSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsMolFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesDupeFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesOutput' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Output' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Supply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Transform' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'rdBase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.utils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.NodeLib.rst [autosectionlabel.source/rdkit.utils] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.utils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.NodeLib.rst [autosectionlabel.source/rdkit.utils] WARNING: autodoc: failed to import module 'utils.cactvs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.chemutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.fileutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.listutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.spiral' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/rdkit-202409.6/Docs/Book/data/README.md: WARNING: document isn't included in any toctree done preparing documents... done copying assets... copying downloadable files... [ 5%] C++Examples/example1.cpp copying downloadable files... [ 11%] C++Examples/example2.cpp copying downloadable files... [ 16%] C++Examples/example3.cpp copying downloadable files... [ 21%] C++Examples/example4.cpp copying downloadable files... [ 26%] C++Examples/example5.cpp copying downloadable files... [ 32%] C++Examples/example6.cpp copying downloadable files... [ 37%] C++Examples/example7.cpp copying downloadable files... [ 42%] C++Examples/example8.cpp copying downloadable files... [ 47%] C++Examples/example9.cpp copying downloadable files... [ 53%] ../Code/GraphMol/Bond.h copying downloadable files... [ 58%] C++Examples/example10.cpp copying downloadable files... [ 63%] C++Examples/CMakeLists.txt copying downloadable files... [ 68%] C++Examples/example11.cpp copying downloadable files... [ 74%] C++Examples/example12.cpp copying downloadable files... [ 79%] C++Examples/example13.cpp copying downloadable files... [ 84%] C++Examples/example17.cpp copying downloadable files... [ 89%] C++Examples/example14.cpp copying downloadable files... [ 95%] C++Examples/example15.cpp copying downloadable files... [100%] C++Examples/example16.cpp copying static files... Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/html/_static/basic.css Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/html/_static/sphinxdoc.css copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 0%] BackwardsIncompatibleChanges writing output... [ 1%] Cartridge writing output... [ 1%] Cookbook writing output... [ 2%] GettingStartedInC++ writing output... [ 2%] GettingStartedInPython writing output... [ 2%] GettingStartedWithContributing writing output... [ 3%] Install writing output... [ 3%] Overview writing output... [ 3%] RDKit_Book writing output... [ 4%] api-docs writing output... [ 4%] data/README writing output... [ 5%] index writing output... [ 5%] source/rdkit writing output... [ 5%] source/rdkit.Avalon writing output... [ 6%] source/rdkit.Avalon.pyAvalonTools writing output... [ 6%] source/rdkit.Chem writing output... [ 6%] source/rdkit.Chem.AllChem writing output... [ 7%] source/rdkit.Chem.AtomPairs writing output... [ 7%] source/rdkit.Chem.AtomPairs.Pairs writing output... [ 8%] source/rdkit.Chem.AtomPairs.Sheridan writing output... [ 8%] source/rdkit.Chem.AtomPairs.Torsions writing output... [ 8%] source/rdkit.Chem.AtomPairs.Utils writing output... [ 9%] source/rdkit.Chem.BRICS writing output... [ 9%] source/rdkit.Chem.BuildFragmentCatalog writing output... [ 10%] source/rdkit.Chem.ChemUtils writing output... 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The HTML pages are in _build/html. make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.6/Docs/Book' (cd /build/reproducible-path/rdkit-202409.6/Docs/Book; RDBASE=/build/reproducible-path/rdkit-202409.6 /usr/bin/make latexpdf) make[2]: Entering directory '/build/reproducible-path/rdkit-202409.6/Docs/Book' mkdir -p _build/html/cppapi cp -r /build/reproducible-path/rdkit-202409.6/Code/docs/* _build/html/cppapi sphinx-build -b latex -d _build/doctrees . _build/latex Running Sphinx v8.1.3 loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist loading pickled environment... done myst v4.0.1: 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_sort=True, 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 [latex]: all documents updating environment: 0 added, 249 changed, 0 removed reading sources... 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[100%] source/rdkit.utils.spiral WARNING: autodoc: failed to import module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst [autosectionlabel.source/rdkit] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.rst:24: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.utils.rst [autosectionlabel.source/rdkit] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.rst:36: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.utils.rst [autosectionlabel.source/rdkit] WARNING: autodoc: failed to import module 'Avalon' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Avalon.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Avalon] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Avalon.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Avalon] WARNING: autodoc: failed to import module 'Avalon.pyAvalonTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Chem] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst:28: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Avalon.rst [autosectionlabel.source/rdkit.Chem] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst:115: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Avalon.rst [autosectionlabel.source/rdkit.Chem] WARNING: autodoc: failed to import module 'Chem.AllChem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.AtomPairs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.Chem.AtomPairs] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.AtomPairs.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.Chem.AtomPairs] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Pairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Sheridan' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Torsions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.BRICS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.BuildFragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.ChemUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.AtomPairs.rst [autosectionlabel.source/rdkit.Chem.ChemUtils] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.ChemUtils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.AtomPairs.rst [autosectionlabel.source/rdkit.Chem.ChemUtils] WARNING: autodoc: failed to import module 'Chem.ChemUtils.AlignDepict' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.BulkTester' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.DescriptorUtilities' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.SDFToCSV' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.TemplateExpand' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemicalForceFields' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Crippen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Descriptors3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Draw.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.ChemUtils.rst [autosectionlabel.source/rdkit.Chem.Draw] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Draw.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.ChemUtils.rst [autosectionlabel.source/rdkit.Chem.Draw] WARNING: autodoc: failed to import module 'Chem.Draw.IPythonConsole' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.MolDrawing' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.SimilarityMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2DQt' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.EState.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Draw.rst [autosectionlabel.source/rdkit.Chem.EState] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.EState.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Draw.rst [autosectionlabel.source/rdkit.Chem.EState] WARNING: autodoc: failed to import module 'Chem.EState.AtomTypes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState.EState_VSA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState.Fingerprinter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EnumerateHeterocycles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EnumerateStereoisomers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FastSDMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatFinderCLI' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.FeatMaps.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.EState.rst [autosectionlabel.source/rdkit.Chem.FeatMaps] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.FeatMaps.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.EState.rst [autosectionlabel.source/rdkit.Chem.FeatMaps] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapParser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapPoint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Features' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Features.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.FeatMaps.rst [autosectionlabel.source/rdkit.Chem.Features] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Features.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.FeatMaps.rst [autosectionlabel.source/rdkit.Chem.Features] WARNING: autodoc: failed to import module 'Chem.Features.FeatDirUtilsRD' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Features.ShowFeats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FilterCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fingerprints.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Features.rst [autosectionlabel.source/rdkit.Chem.Fingerprints] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fingerprints.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Features.rst [autosectionlabel.source/rdkit.Chem.Fingerprints] WARNING: autodoc: failed to import module 'Chem.Fingerprints.ClusterMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.DbFpSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.FingerprintMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.MolSimilarity' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.SimilarityScreener' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fraggle' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fraggle.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fingerprints.rst [autosectionlabel.source/rdkit.Chem.Fraggle] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fraggle.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fingerprints.rst [autosectionlabel.source/rdkit.Chem.Fraggle] WARNING: autodoc: failed to import module 'Chem.Fraggle.FraggleSim' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FragmentMatcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fragments' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FunctionalGroups' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.GraphDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Graphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Lipinski' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MACCSkeys' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolDb.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fraggle.rst [autosectionlabel.source/rdkit.Chem.MolDb] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolDb.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fraggle.rst [autosectionlabel.source/rdkit.Chem.MolDb] WARNING: autodoc: failed to import module 'Chem.MolDb.FingerprintUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb.Loader' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_orig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_sa' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolKey.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolDb.rst [autosectionlabel.source/rdkit.Chem.MolKey] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolKey.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolDb.rst [autosectionlabel.source/rdkit.Chem.MolKey] WARNING: autodoc: failed to import module 'Chem.MolKey.InchiInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolKey.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolStandardize.rdMolStandardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolSurf' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PandasTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PeriodicTable' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm2D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolKey.rst [autosectionlabel.source/rdkit.Chem.Pharm2D] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm2D.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolKey.rst [autosectionlabel.source/rdkit.Chem.Pharm2D] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Generate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Gobbi_Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Matcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.SigFactory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm3D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm2D.rst [autosectionlabel.source/rdkit.Chem.Pharm3D] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm3D.rst:14: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm2D.rst [autosectionlabel.source/rdkit.Chem.Pharm3D] WARNING: autodoc: failed to import module 'Chem.Pharm3D.EmbedLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm3D.ExcludedVolume' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm3D.Pharmacophore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PropertyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.QED' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Randomize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Recap' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.RegistrationHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SATIS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SaltRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Scaffolds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Scaffolds.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm3D.rst [autosectionlabel.source/rdkit.Chem.Scaffolds] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Scaffolds.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm3D.rst [autosectionlabel.source/rdkit.Chem.Scaffolds] WARNING: autodoc: failed to import module 'Chem.Scaffolds.MurckoScaffold' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Scaffolds.rdScaffoldNetwork' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ShowMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SimpleEnum' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Scaffolds.rst [autosectionlabel.source/rdkit.Chem.SimpleEnum] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Scaffolds.rst [autosectionlabel.source/rdkit.Chem.SimpleEnum] WARNING: autodoc: failed to import module 'Chem.SimpleEnum.Enumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SpacialScore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Subshape.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.SimpleEnum.rst [autosectionlabel.source/rdkit.Chem.Subshape] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Subshape.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.SimpleEnum.rst [autosectionlabel.source/rdkit.Chem.Subshape] WARNING: autodoc: failed to import module 'Chem.Subshape.BuilderUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeAligner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeBuilder' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeObjects' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Suppliers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Suppliers.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Subshape.rst [autosectionlabel.source/rdkit.Chem.Suppliers] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Suppliers.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Subshape.rst [autosectionlabel.source/rdkit.Chem.Suppliers] WARNING: autodoc: failed to import module 'Chem.Suppliers.DbMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Suppliers.MolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.TemplateAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.TorsionFingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.fmcs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Suppliers.rst [autosectionlabel.source/rdkit.Chem.fmcs] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.fmcs.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Suppliers.rst [autosectionlabel.source/rdkit.Chem.fmcs] WARNING: autodoc: failed to import module 'Chem.fmcs.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.inchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdAbbreviations' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdCIPLabeler' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdChemReactions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdCoordGen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDepictor' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDeprotect' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDetermineBonds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdEHTTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdFMCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdFingerprintGenerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdForceFieldHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdFreeSASA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMHFPFingerprint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMMPA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolEnumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolInterchange' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolTransforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdPartialCharges' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdRGroupDecomposition' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdSLNParse' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdShapeAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdShapeHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdSubstructLibrary' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdSynthonSpaceSearch' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdTautomerQuery' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdchem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdfiltercatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdfragcatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdinchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdmolfiles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdmolops' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdqueries' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdtrajectory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataManip' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.DataManip] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.fmcs.rst [autosectionlabel.source/rdkit.DataManip] WARNING: autodoc: failed to import module 'DataManip.Metric' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.Metric.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.fmcs.rst [autosectionlabel.source/rdkit.DataManip.Metric] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.Metric.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.rst [autosectionlabel.source/rdkit.DataManip.Metric] WARNING: autodoc: failed to import module 'DataManip.Metric.rdMetricMatrixCalc' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataStructs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.Metric.rst [autosectionlabel.source/rdkit.DataStructs] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataStructs.rst:18: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.Metric.rst [autosectionlabel.source/rdkit.DataStructs] WARNING: autodoc: failed to import module 'DataStructs.BitEnsemble' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.BitEnsembleDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.BitUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.LazySignature' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.TopNContainer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.VectCollection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.cDataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Dbase.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataStructs.rst [autosectionlabel.source/rdkit.Dbase] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Dbase.rst:17: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataStructs.rst [autosectionlabel.source/rdkit.Dbase] WARNING: autodoc: failed to import module 'Dbase.DbConnection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbModule' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbResultSet' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.StorageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DistanceGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DistanceGeometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Dbase.rst [autosectionlabel.source/rdkit.DistanceGeometry] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DistanceGeometry.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Dbase.rst [autosectionlabel.source/rdkit.DistanceGeometry] WARNING: autodoc: failed to import module 'DistanceGeometry.DistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ForceField.rst:5: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] WARNING: autodoc: failed to import module 'ForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ForceField.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DistanceGeometry.rst [autosectionlabel.source/rdkit.ForceField] WARNING: autodoc: failed to import module 'ForceField.rdForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Geometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Geometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DistanceGeometry.rst [autosectionlabel.source/rdkit.Geometry] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Geometry.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ForceField.rst [autosectionlabel.source/rdkit.Geometry] WARNING: autodoc: failed to import module 'Geometry.rdGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.rst [autosectionlabel.source/rdkit.ML] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst:18: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Geometry.rst [autosectionlabel.source/rdkit.ML] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst:26: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Geometry.rst [autosectionlabel.source/rdkit.ML] WARNING: autodoc: failed to import module 'ML.Cluster' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Cluster.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.ML.Cluster] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Cluster.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.ML.Cluster] WARNING: autodoc: failed to import module 'ML.Cluster.Butina' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.ClusterUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.ClusterVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Clustering' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Clusters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Murtagh' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Resemblance' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Standardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Data.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Cluster.rst [autosectionlabel.source/rdkit.ML.Data] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Data.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Cluster.rst [autosectionlabel.source/rdkit.ML.Data] WARNING: autodoc: failed to import module 'ML.Data.DataUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.FindQuantBounds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.MLData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.Quantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.SplitData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.Stats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.Transforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.cQuantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Descriptors.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Data.rst [autosectionlabel.source/rdkit.ML.Descriptors] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Descriptors.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Data.rst [autosectionlabel.source/rdkit.ML.Descriptors] WARNING: autodoc: failed to import module 'ML.Descriptors.CompoundDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors.MoleculeDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors.Parser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.InfoTheory.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Descriptors.rst [autosectionlabel.source/rdkit.ML.InfoTheory] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.InfoTheory.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Descriptors.rst [autosectionlabel.source/rdkit.ML.InfoTheory] WARNING: autodoc: failed to import module 'ML.InfoTheory.BitClusterer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory.BitRank' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory.entropy' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory.rdInfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.MLUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.MLUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.InfoTheory.rst [autosectionlabel.source/rdkit.ML.MLUtils] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.MLUtils.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.InfoTheory.rst [autosectionlabel.source/rdkit.ML.MLUtils] WARNING: autodoc: failed to import module 'ML.MLUtils.VoteImg' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.MatOps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.SLT' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.SLT.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.MLUtils.rst [autosectionlabel.source/rdkit.ML.SLT] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.SLT.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.MLUtils.rst [autosectionlabel.source/rdkit.ML.SLT] WARNING: autodoc: failed to import module 'ML.SLT.Risk' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Scoring.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.SLT.rst [autosectionlabel.source/rdkit.ML.Scoring] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Scoring.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.SLT.rst [autosectionlabel.source/rdkit.ML.Scoring] WARNING: autodoc: failed to import module 'ML.Scoring.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.files' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Numerics' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Numerics.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Scoring.rst [autosectionlabel.source/rdkit.Numerics] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Numerics.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Scoring.rst [autosectionlabel.source/rdkit.Numerics] WARNING: autodoc: failed to import module 'Numerics.rdAlignment' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDConfig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDLogger' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDPaths' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDRandom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'SimDivFilters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.SimDivFilters.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Numerics.rst [autosectionlabel.source/rdkit.SimDivFilters] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.SimDivFilters.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Numerics.rst [autosectionlabel.source/rdkit.SimDivFilters] WARNING: autodoc: failed to import module 'SimDivFilters.SimilarityPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'SimDivFilters.rdSimDivPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'TestRunner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.VLib] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst:12: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.SimDivFilters.rst [autosectionlabel.source/rdkit.VLib] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst:23: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.SimDivFilters.rst [autosectionlabel.source/rdkit.VLib] WARNING: autodoc: failed to import module 'VLib.Filter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Node' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.NodeLib.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst [autosectionlabel.source/rdkit.VLib.NodeLib] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.NodeLib.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst [autosectionlabel.source/rdkit.VLib.NodeLib] WARNING: autodoc: failed to import module 'VLib.NodeLib.DbMolSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.DbPickleSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SDSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsMolFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesDupeFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesOutput' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Output' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Supply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Transform' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'rdBase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.utils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.NodeLib.rst [autosectionlabel.source/rdkit.utils] /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.utils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.NodeLib.rst [autosectionlabel.source/rdkit.utils] WARNING: autodoc: failed to import module 'utils.cactvs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.chemutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.fileutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.listutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.spiral' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/rdkit-202409.6/Docs/Book/data/README.md: WARNING: document isn't included in any toctree done preparing documents... done copying assets... copying TeX support files... Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex/make.bat Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex/latexmkrc Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex/latexmkjarc Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex/Makefile done copying assets: done processing RDKit.tex... index Overview Install GettingStartedInPython RDKit_Book GettingStartedWithContributing Cookbook Cartridge BackwardsIncompatibleChanges api-docs source/rdkit source/rdkit.Avalon source/rdkit.Avalon.pyAvalonTools source/rdkit.Chem source/rdkit.Chem.AtomPairs source/rdkit.Chem.AtomPairs.Pairs source/rdkit.Chem.AtomPairs.Sheridan source/rdkit.Chem.AtomPairs.Torsions source/rdkit.Chem.AtomPairs.Utils source/rdkit.Chem.ChemUtils source/rdkit.Chem.ChemUtils.AlignDepict source/rdkit.Chem.ChemUtils.BulkTester source/rdkit.Chem.ChemUtils.DescriptorUtilities source/rdkit.Chem.ChemUtils.SDFToCSV source/rdkit.Chem.ChemUtils.TemplateExpand source/rdkit.Chem.Draw source/rdkit.Chem.Draw.IPythonConsole source/rdkit.Chem.Draw.MolDrawing source/rdkit.Chem.Draw.SimilarityMaps source/rdkit.Chem.Draw.rdMolDraw2D source/rdkit.Chem.Draw.rdMolDraw2DQt source/rdkit.Chem.EState source/rdkit.Chem.EState.AtomTypes source/rdkit.Chem.EState.EState source/rdkit.Chem.EState.EState_VSA source/rdkit.Chem.EState.Fingerprinter source/rdkit.Chem.FeatMaps source/rdkit.Chem.FeatMaps.FeatMapParser source/rdkit.Chem.FeatMaps.FeatMapPoint source/rdkit.Chem.FeatMaps.FeatMapUtils source/rdkit.Chem.FeatMaps.FeatMaps source/rdkit.Chem.Features source/rdkit.Chem.Features.FeatDirUtilsRD source/rdkit.Chem.Features.ShowFeats source/rdkit.Chem.Fingerprints source/rdkit.Chem.Fingerprints.ClusterMols source/rdkit.Chem.Fingerprints.DbFpSupplier source/rdkit.Chem.Fingerprints.FingerprintMols source/rdkit.Chem.Fingerprints.MolSimilarity source/rdkit.Chem.Fingerprints.SimilarityScreener source/rdkit.Chem.Fraggle source/rdkit.Chem.Fraggle.FraggleSim source/rdkit.Chem.MolDb source/rdkit.Chem.MolDb.FingerprintUtils source/rdkit.Chem.MolDb.Loader source/rdkit.Chem.MolDb.Loader_orig source/rdkit.Chem.MolDb.Loader_sa source/rdkit.Chem.MolKey source/rdkit.Chem.MolKey.InchiInfo source/rdkit.Chem.MolKey.MolKey source/rdkit.Chem.Pharm2D source/rdkit.Chem.Pharm2D.Generate source/rdkit.Chem.Pharm2D.Gobbi_Pharm2D source/rdkit.Chem.Pharm2D.Matcher source/rdkit.Chem.Pharm2D.SigFactory source/rdkit.Chem.Pharm2D.Utils source/rdkit.Chem.Pharm3D source/rdkit.Chem.Pharm3D.EmbedLib source/rdkit.Chem.Pharm3D.ExcludedVolume source/rdkit.Chem.Pharm3D.Pharmacophore source/rdkit.Chem.Scaffolds source/rdkit.Chem.Scaffolds.MurckoScaffold source/rdkit.Chem.Scaffolds.rdScaffoldNetwork source/rdkit.Chem.SimpleEnum source/rdkit.Chem.SimpleEnum.Enumerator source/rdkit.Chem.Subshape source/rdkit.Chem.Subshape.BuilderUtils source/rdkit.Chem.Subshape.SubshapeAligner source/rdkit.Chem.Subshape.SubshapeBuilder source/rdkit.Chem.Subshape.SubshapeObjects source/rdkit.Chem.Suppliers source/rdkit.Chem.Suppliers.DbMolSupplier source/rdkit.Chem.Suppliers.MolSupplier source/rdkit.Chem.fmcs source/rdkit.Chem.fmcs.fmcs source/rdkit.Chem.AllChem source/rdkit.Chem.BRICS source/rdkit.Chem.BuildFragmentCatalog source/rdkit.Chem.ChemicalFeatures source/rdkit.Chem.ChemicalForceFields source/rdkit.Chem.Crippen source/rdkit.Chem.Descriptors source/rdkit.Chem.Descriptors3D source/rdkit.Chem.EnumerateHeterocycles source/rdkit.Chem.EnumerateStereoisomers source/rdkit.Chem.FastSDMolSupplier source/rdkit.Chem.FeatFinderCLI source/rdkit.Chem.FilterCatalog source/rdkit.Chem.FragmentCatalog source/rdkit.Chem.FragmentMatcher source/rdkit.Chem.Fragments source/rdkit.Chem.FunctionalGroups source/rdkit.Chem.GraphDescriptors source/rdkit.Chem.Graphs source/rdkit.Chem.Lipinski source/rdkit.Chem.MACCSkeys source/rdkit.Chem.MolCatalog source/rdkit.Chem.MolStandardize source/rdkit.Chem.MolStandardize.rdMolStandardize source/rdkit.Chem.MolSurf source/rdkit.Chem.PandasTools source/rdkit.Chem.PeriodicTable source/rdkit.Chem.PropertyMol source/rdkit.Chem.PyMol source/rdkit.Chem.QED source/rdkit.Chem.Randomize source/rdkit.Chem.Recap source/rdkit.Chem.ReducedGraphs source/rdkit.Chem.RegistrationHash source/rdkit.Chem.SATIS source/rdkit.Chem.SaltRemover source/rdkit.Chem.ShowMols source/rdkit.Chem.SpacialScore source/rdkit.Chem.TemplateAlign source/rdkit.Chem.TorsionFingerprints source/rdkit.Chem.inchi source/rdkit.Chem.rdchem source/rdkit.Chem.rdDistGeom source/rdkit.Chem.rdqueries source/rdkit.Chem.rdFMCS source/rdkit.Chem.rdMolAlign source/rdkit.Chem.rdMolHash source/rdkit.Chem.rdReducedGraphs source/rdkit.Chem.rdtrajectory source/rdkit.Chem.rdMolTransforms source/rdkit.Chem.rdmolfiles source/rdkit.Chem.rdPartialCharges source/rdkit.Chem.rdMolCatalog source/rdkit.Chem.rdCoordGen source/rdkit.Chem.rdMolChemicalFeatures source/rdkit.Chem.rdMMPA source/rdkit.Chem.rdRGroupDecomposition source/rdkit.Chem.rdForceFieldHelpers source/rdkit.Chem.rdDepictor source/rdkit.Chem.rdChemicalFeatures source/rdkit.Chem.rdmolops source/rdkit.Chem.rdFreeSASA source/rdkit.Chem.rdMolInterchange source/rdkit.Chem.rdShapeHelpers source/rdkit.Chem.rdinchi source/rdkit.Chem.rdChemReactions source/rdkit.Chem.rdSubstructLibrary source/rdkit.Chem.rdfiltercatalog source/rdkit.Chem.rdfragcatalog source/rdkit.Chem.rdMolDescriptors source/rdkit.Chem.rdFingerprintGenerator source/rdkit.Chem.rdMHFPFingerprint source/rdkit.Chem.rdSLNParse source/rdkit.Chem.rdAbbreviations source/rdkit.Chem.rdDeprotect source/rdkit.Chem.rdMolEnumerator source/rdkit.Chem.rdCIPLabeler source/rdkit.Chem.rdTautomerQuery source/rdkit.Chem.rdEHTTools source/rdkit.Chem.rdDetermineBonds source/rdkit.Chem.rdShapeAlign source/rdkit.Chem.rdSynthonSpaceSearch source/rdkit.DataManip source/rdkit.DataManip.Metric source/rdkit.DataManip.Metric.rdMetricMatrixCalc source/rdkit.DataStructs source/rdkit.DataStructs.BitEnsemble source/rdkit.DataStructs.BitEnsembleDb source/rdkit.DataStructs.BitUtils source/rdkit.DataStructs.LazySignature source/rdkit.DataStructs.TopNContainer source/rdkit.DataStructs.VectCollection source/rdkit.DataStructs.cDataStructs source/rdkit.Dbase source/rdkit.Dbase.DbConnection source/rdkit.Dbase.DbInfo source/rdkit.Dbase.DbModule source/rdkit.Dbase.DbResultSet source/rdkit.Dbase.DbUtils source/rdkit.Dbase.StorageUtils source/rdkit.DistanceGeometry source/rdkit.DistanceGeometry.DistGeom source/rdkit.ForceField source/rdkit.ForceField.rdForceField source/rdkit.Geometry source/rdkit.Geometry.rdGeometry source/rdkit.ML source/rdkit.ML.Cluster source/rdkit.ML.Cluster.Butina source/rdkit.ML.Cluster.ClusterUtils source/rdkit.ML.Cluster.ClusterVis source/rdkit.ML.Cluster.Clusters source/rdkit.ML.Cluster.Murtagh source/rdkit.ML.Cluster.Resemblance source/rdkit.ML.Cluster.Standardize source/rdkit.ML.Cluster.Clustering source/rdkit.ML.Data source/rdkit.ML.Data.DataUtils source/rdkit.ML.Data.FindQuantBounds source/rdkit.ML.Data.MLData source/rdkit.ML.Data.Quantize source/rdkit.ML.Data.cQuantize source/rdkit.ML.Data.SplitData source/rdkit.ML.Data.Stats source/rdkit.ML.Data.Transforms source/rdkit.ML.Descriptors source/rdkit.ML.Descriptors.CompoundDescriptors source/rdkit.ML.Descriptors.Descriptors source/rdkit.ML.Descriptors.MoleculeDescriptors source/rdkit.ML.Descriptors.Parser source/rdkit.ML.InfoTheory source/rdkit.ML.InfoTheory.BitClusterer source/rdkit.ML.InfoTheory.BitRank source/rdkit.ML.InfoTheory.entropy source/rdkit.ML.InfoTheory.rdInfoTheory source/rdkit.ML.MLUtils source/rdkit.ML.MLUtils.VoteImg source/rdkit.ML.SLT source/rdkit.ML.SLT.Risk source/rdkit.ML.Scoring source/rdkit.ML.Scoring.Scoring source/rdkit.ML.MatOps source/rdkit.ML.files source/rdkit.Numerics source/rdkit.Numerics.rdAlignment source/rdkit.SimDivFilters source/rdkit.SimDivFilters.SimilarityPickers source/rdkit.SimDivFilters.rdSimDivPickers source/rdkit.VLib source/rdkit.VLib.NodeLib source/rdkit.VLib.NodeLib.DbMolSupply source/rdkit.VLib.NodeLib.DbPickleSupplier source/rdkit.VLib.NodeLib.SDSupply source/rdkit.VLib.NodeLib.SmartsMolFilter source/rdkit.VLib.NodeLib.SmartsRemover source/rdkit.VLib.NodeLib.SmilesDupeFilter source/rdkit.VLib.NodeLib.SmilesOutput source/rdkit.VLib.NodeLib.SmilesSupply source/rdkit.VLib.Filter source/rdkit.VLib.Node source/rdkit.VLib.Output source/rdkit.VLib.Supply source/rdkit.VLib.Transform source/rdkit.utils source/rdkit.utils.cactvs source/rdkit.utils.chemutils source/rdkit.utils.fileutils source/rdkit.utils.listutils source/rdkit.utils.spiral source/rdkit.rdBase source/rdkit.RDConfig source/rdkit.RDLogger source/rdkit.RDPaths source/rdkit.RDRandom source/rdkit.TestRunner GettingStartedInC++ resolving references... /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md:273: WARNING: 'myst' cross-reference target not found: 'building-rdkit-for-development' [myst.xref_missing] WARNING: Could not fetch remote image: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: 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[1] [2] Chapter 1. (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) Underfull \hbox (badness 10000) in paragraph at lines 131--133 []\T1/qtm/m/n/10 Chem-in-for-mat-ics nodes for KN-IME (dis-tributed from the KN -IME com-mu-nity site: [1{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) [2] Chapter 2. [3] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [4] [5] [6] Underfull \hbox (badness 10000) in paragraph at lines 636--638 []\T1/qtm/m/n/10 If you want to use the python wrap-pers: \T1/txtt/m/n/10 ./boo tstrap.sh [][]with[]libraries=python, [7] [8] Underfull \hbox (badness 10000) in paragraph at lines 803--805 []\T1/qtm/m/n/10 You can en-able sup-port for gen-er-at-ing InChI strings and I nChI keys by adding the ar-gu-ment [9] [10] Underfull \hbox (badness 5490) in paragraph at lines 1028--1030 \T1/qtm/m/n/10 This sec-tion as-sumes that python is in-stalled in \T1/txtt/m/n /10 C:[]Python36 that the boost libraries have been [11] Underfull \hbox (badness 10000) in paragraph at lines 1079--1082 []\T1/txtt/m/n/10 DBOOST_ROOT=C:/boost []DRDK_BUILD_INCHI_SUPPORT=ON []DRDK_BUI LD_AVALON_SUPPORT=ON Underfull \hbox (badness 10000) in paragraph at lines 1079--1082 []\T1/txtt/m/n/10 DRDK_BUILD_PGSQL=ON []DPostgreSQL_ROOT="C:[]Program Files[]Po stgreSQL[]9.5" []G"Visual Underfull \hbox (badness 10000) in paragraph at lines 1093--1095 []\T1/txtt/m/n/10 "C:[]Program Files[]PostgreSQL[]9.5[]bin[]pg_ctl.exe" []N "po stgresql[]9.5" []D "C:[] Underfull \hbox (badness 10000) in paragraph at lines 1101--1103 []\T1/txtt/m/n/10 "C:[]Program Files[]PostgreSQL[]9.5[]bin[]pg_ctl.exe" []N "po stgresql[]9.5" []D "C:[] [12] Chapter 3. [13] [14 <./Cc1ccccc1.png>] [15] [16] LaTeX Warning: Hyper reference `GettingStartedInPython:chem-vs-allchem' on page 17 undefined on input line 1446. [17] [18] [19] [20] LaTeX Warning: Hyper reference `GettingStartedInPython:the-sssr-problem' on pag e 21 undefined on input line 1686. [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 1836--1839 []\T1/qtm/m/n/10 An-other op-tion for Com-pute2DCoords al-lows you to gen-er-at e 2D de-pic-tions for molecules that Underfull \hbox (badness 10000) in paragraph at lines 1836--1839 \T1/qtm/m/n/10 closely mimic 3D con-form-ers. This is avail-able us-ing the fun c-tion \T1/txtt/m/n/10 rdkit.Chem.AllChem. Underfull \hbox (badness 10000) in paragraph at lines 1861--1867 []\T1/qtm/m/n/10 More fine-grained con-trol can be ob-tained us-ing the core fu nc-tion \T1/txtt/m/n/10 rdkit.Chem.rdDepictor. 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[38] [39] [40 <./mcs_example_1.png> <./mcs_example_2.png>] [41 <./mcs_example_3.png> <./mcs_example_4.png>] [42 <./mcs_example_5.png> <./mcs_example_6.png>] [43] [44] [45] [46] [47] [48] LaTeX Warning: Hyper reference `GettingStartedInPython:feature-definitions-used -in-the-morgan-fingerprints' on page 49 undefined on input line 3358. [49] [50] [51] [52] [53 <./mfp2_bit872.png> <./rdk_bit1553.png>] [54 <./rdk_bit1553_2.png>] [55] [56 <./similarity_map_fp1.png>] [57 <./similarity_map_fp2.png>] LaTeX Warning: Hyper reference `GettingStartedInPython:list-of-available-descri ptors' on page 58 undefined on input line 3866. Overfull \vbox (1.67828pt too high) detected at line 3879 [58 <./similarity_map_fp3.png>] [59] [60 <./similarity_map_charges.png>] LaTeX Warning: Hyper reference `RDKit_Book::doc' on page 61 undefined on input line 3975. 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[96] [97 <./parastereo_2.png> <./parastereo_1.png> <./potential_stereo_double_bond1. png> <./potential_stereo_double_bond2.png>] [98 <./potential_stereo_double_bond3.png>] [99] [100 <./nontetstereo_sp1.png> <./nontetstereo_sp2.png> <./nontetstereo_sp3.png> <./nontetstereo_sp4.png>] [101 <./nontetstereo_tb2.png> <./nontetstereo_tb1.png>] Package longtable Warning: Column widths have changed (longtable) in table 1 on input line 9400. [102 <./nontetstereo_oh2.png> <./nontetstereo_oh1.png>] Underfull \hbox (badness 10000) in paragraph at lines 9413--9415 []\T1/qtm/m/n/10 The clas-sic ex-am-ple of this is cis-platin - \T1/txtt/m/n/10 Cl[Pt@SP1](Cl)(<[][NH3])<[][NH3] \T1/qtm/m/n/10 - vs trans-platin - [103 <./nontetstereo_ex1.png> <./nontetstereo_ex2.png> <./nontetstereo_missing1 .png>] [104] [105] [106] [107] [108] [109] LaTeX Warning: Hyper reference `RDKit_Book:ph4-figure' on page 110 undefined on input line 9970. 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[113 <./ary_group.png>] [114] [115] Underfull \hbox (badness 10000) in paragraph at lines 10871--10873 \T1/qtm/m/n/10 Here's the rd-kitj-son rep-re-sen-ta-tion of the stereo groups f rom the molecule [116] Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 _Chi-ral-i-ty-Pos-si- Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 _Re-ac-tion-De- Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 mo-lAtomMap- Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 molFileIn-ver- Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 mol-Rxn-Com-po- [117] [118] Underfull \hbox (badness 10000) in paragraph at lines 11271--11276 []\T1/qtm/m/n/10 By de-fault the \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles.SDMolSup plier \T1/qtm/m/n/10 and \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles. 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[151] [152 <./RDKitCB_0_im0.png> <./RDKitCB_0_im1.png>] [153 <./RDKitCB_0_im2.png> <./RDKitCB_40_im0.png>] [154 <./RDKitCB_40_im1.png> <./RDKitCB_23_im0.png>] [155 <./RDKitCB_23_im1.png> <./RDKitCB_32_im0.png>] [156 <./RDKitCB_32_im1.png> <./RDKitCB_1_im0.png (PNG copy)>] [157 <./RDKitCB_1_im1.png (PNG copy)> <./RDKitCB_1_im2.png (PNG copy)>] [158 <./RDKitCB_1_im3.png (PNG copy)> <./RDKitCB_2_im0.png>] [159 <./RDKitCB_2_im1.png> <./RDKitCB_36_im0.png>] [160 <./RDKitCB_36_im1.png>] [161 <./RDKitCB_38_im0.png>] [162 <./RDKitCB_39_im0.png (PNG copy)>] [163 <./RDKitCB_17_im0.png> <./RDKitCB_17_im1.png>] [164 <./RDKitCB_34_im0.png> <./RDKitCB_34_im1.png> <./RDKitCB_34_im2.png>] [165] Overfull \hbox (396.49246pt too wide) in paragraph at lines 14208--14208 []\T1/txtt/m/n/10 CC(C)C(O)C1C(=O)NC(CC)C(=O)N(C)CC(=O)N(C)C(CC(C)C)C(=O)NC(C(C )C)C(=O)N(C)C(CC(C)C)C(=O)NC(C)C(=O)NC(C)C(=O)N(C)C(CC(C)C)C(=O)N(C)C(CC(C)C)C( =O)N(C)C(C(C)C)C(=O)N1C[][] [166 <./RDKitCB_37_im0.png>] Overfull \hbox (396.49246pt too wide) in paragraph at lines 14237--14237 []\T1/txtt/m/n/10 CC(C)C(O)C1C(=O)NC(CC)C(=O)N(C)CC(=O)N(C)C(CC(C)C)C(=O)NC(C(C )C)C(=O)N(C)C(CC(C)C)C(=O)NC(C)C(=O)NC(C)C(=O)N(C)C(CC(C)C)C(=O)N(C)C(CC(C)C)C( =O)N(C)C(C(C)C)C(=O)N1C[][] [167 <./RDKitCB_37_im1.png>] [168 <./RDKitCB_37_im2.png>] [169 <./RDKitCB_35_im0.png>] [170] [171 <./RDKitCB_3_im0.png> <./RDKitCB_8_im0.png>] [172] [173 <./RDKitCB_30_im0.png>] [174 <./RDKitCB_30_im1.png>] [175 <./RDKitCB_7_im0.png> <./RDKitCB_7_im1.png>] [176 <./RDKitCB_7_im2.png (PNG copy)> <./RDKitCB_7_im3.png> <./RDKitCB_7_im4.pn g>] [177 <./RDKitCB_7_im5.png> <./RDKitCB_7_im6.png (PNG copy)>] [178] [179] [180 <./RDKitCB_29_im0.png (PNG copy)>] Underfull \vbox (badness 1043) detected at line 14891 [181 <./RDKitCB_33_im0.png (PNG copy)>] Overfull \vbox (0.99814pt too high) detected at line 14926 [182 <./RDKitCB_33_im1.png (PNG copy)>] [183 <./RDKitCB_33_im2.png (PNG copy)>] Overfull \hbox (490.99219pt too wide) in paragraph at lines 14992--14992 []\T1/txtt/m/n/10 "[][]CC[C@@H]1[C@@]([C@@H]([C@H](C(=O)[C@@H](C[C@@]([C@@H]([C @H]([C@@H]([C@H](C(=O)O1)C)O[C@H]2C[C@@]([C@H]([C@@H](O2)C)O)(C)OC)C)O[C@H]3[C@ @H]([C@H](C[C@H](O3)C)N(C)C)O)(C)O)C)C)O)(C)O[][] [184 <./RDKitCB_13_im0.png>] [185 <./RDKitCB_13_im1.png>] [186] [187 <./RDKitCB_20_im0.png>] [188 <./RDKitCB_21_im0.png>] [189 <./RDKitCB_21_im1.png>] [190 <./RDKitCB_21_im2.png (PNG copy)> <./RDKitCB_21_im3.png>] [191 <./RDKitCB_21_im4.png>] [192 <./RDKitCB_21_im5.png (PNG copy)>] [193 <./RDKitCB_22_im0.png>] [194 <./RDKitCB_22_im1.png>] [195 <./RDKitCB_6_im0.png (PNG copy)>] [196 <./RDKitCB_6_im1.png (PNG copy)> <./RDKitCB_6_im2.png (PNG copy)>] [197] [198 <./RDKitCB_15_im0.png> <./RDKitCB_15_im1.png>] [199] [200] [201] [202 <./RDKitCB_19_im0.png>] [203] [204] [205 <./RDKitCB_28_im0.png (PNG copy)> <./RDKitCB_28_im1.png (PNG copy)>] [206] [207] [208] Chapter 7. 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[229] [230] [231] Underfull \hbox (badness 10000) in paragraph at lines 17791--17795 \T1/qtm/m/n/10 Un-charger::uncharge() will now neu-tral-ize \T1/txtt/m/n/10 [Cl ,Br,I][O[]], [Cl,Br,I](=O)[O[]], [Cl, Underfull \hbox (badness 10000) in paragraph at lines 17791--17795 \T1/txtt/m/n/10 Br,I](=O)(=O)[O[]], [Cl,Br,I](=O)(=O)(=O)[O[]], [O[]]N=N[O[]], [N,P](=O)[O[]], Underfull \hbox (badness 10000) in paragraph at lines 17791--17795 \T1/txtt/m/n/10 [N+](=O)([O[]])[O[]], P(=O)([O[]])[O[]], P(=O)([O[]])([O[]])[O[ ]], S([O[]])[O[]], S(=O)([O[]])[O[]], [232] [233] [234] Chapter 9. [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] Chapter 10. [247] [248] [249] Underfull \hbox (badness 10000) in paragraph at lines 19693--19697 \T1/qtm/m/n/10 Groups of molecules are read us-ing a Sup-plier (for ex-am-ple, an \T1/txtt/m/n/10 RDKit::SDMolSupplier \T1/qtm/m/n/10 or an [250] [251] [252] [253] [254] Overfull \vbox (0.8796pt too high) detected at line 20130 [255] [256] Underfull \hbox (badness 6691) in paragraph at lines 20233--20235 []\T1/qtm/m/n/10 The \T1/txtt/m/n/10 auto\TS1/txtt/m/n/10 ' \T1/txtt/m/n/10 key word here is hiding the fact that \T1/qtm/m/n/10 get-Bond-Be-tweenAtoms\T1/txtt /m/n/10 returns the index of the [257] [258] LaTeX Warning: Hyper reference `GettingStartedInC++:the-sssr-problem' on page 2 59 undefined on input line 20361. LaTeX Warning: Hyper reference `GettingStartedInC++:two-add-hs' on page 259 und efined on input line 20391. [259] [260] [261] [262] [263] [264] [265] [266] [267] [268] Overfull \vbox (1.8739pt too high) detected at line 21250 [269] [270] [271] [272] Chapter 11. [273] [274] Chapter 12. No file RDKit.ind. Package longtable Warning: Table widths have changed. Rerun LaTeX. [275] (./RDKit.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `RDKit.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) Output written on RDKit.pdf (279 pages, 2913721 bytes). Transcript written on RDKit.log. Latexmk: Getting log file 'RDKit.log' Latexmk: Examining 'RDKit.fls' Latexmk: Examining 'RDKit.log' Latexmk: Index file 'RDKit.idx' was written Latexmk: Missing input file 'RDKit.toc' (or dependence on it) from following: No file RDKit.toc. Latexmk: Missing input file 'RDKit.ind' (or dependence on it) from following: No file RDKit.ind. Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'RDKit.pdf' Have index file 'RDKit.idx', RDKit.ind RDKit Latexmk: applying rule 'makeindex RDKit.idx'... Rule 'makeindex RDKit.idx': Reasons for rerun Category 'other': Rerun of 'makeindex RDKit.idx' forced or previously required: Reason or flag: 'Initial set up of rule' ------------ Run number 1 of rule 'makeindex RDKit.idx' ------------ ------------ Running 'makeindex -s python.ist -o "RDKit.ind" "RDKit.idx"' ------------ This is makeindex, version 2.17 [TeX Live 2025/dev] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file RDKit.idx...done (0 entries accepted, 0 rejected). Nothing written in RDKit.ind. Transcript written in RDKit.ilg. Latexmk: applying rule 'pdflatex'... 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(/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) Underfull \hbox (badness 10000) in paragraph at lines 131--133 []\T1/qtm/m/n/10 Chem-in-for-mat-ics nodes for KN-IME (dis-tributed from the KN -IME com-mu-nity site: [1{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) [2] Chapter 2. [3] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [4] [5] [6] Underfull \hbox (badness 10000) in paragraph at lines 636--638 []\T1/qtm/m/n/10 If you want to use the python wrap-pers: \T1/txtt/m/n/10 ./boo tstrap.sh [][]with[]libraries=python, [7] [8] Underfull \hbox (badness 10000) in paragraph at lines 803--805 []\T1/qtm/m/n/10 You can en-able sup-port for gen-er-at-ing InChI strings and I nChI keys by adding the ar-gu-ment [9] [10] Underfull \hbox (badness 5490) in paragraph at lines 1028--1030 \T1/qtm/m/n/10 This sec-tion as-sumes that python is in-stalled in \T1/txtt/m/n /10 C:[]Python36 that the boost libraries have been [11] Underfull \hbox (badness 10000) in paragraph at lines 1079--1082 []\T1/txtt/m/n/10 DBOOST_ROOT=C:/boost []DRDK_BUILD_INCHI_SUPPORT=ON []DRDK_BUI LD_AVALON_SUPPORT=ON Underfull \hbox (badness 10000) in paragraph at lines 1079--1082 []\T1/txtt/m/n/10 DRDK_BUILD_PGSQL=ON []DPostgreSQL_ROOT="C:[]Program Files[]Po stgreSQL[]9.5" []G"Visual Underfull \hbox (badness 10000) in paragraph at lines 1093--1095 []\T1/txtt/m/n/10 "C:[]Program Files[]PostgreSQL[]9.5[]bin[]pg_ctl.exe" []N "po stgresql[]9.5" []D "C:[] Underfull \hbox (badness 10000) in paragraph at lines 1101--1103 []\T1/txtt/m/n/10 "C:[]Program Files[]PostgreSQL[]9.5[]bin[]pg_ctl.exe" []N "po stgresql[]9.5" []D "C:[] [12] Chapter 3. [13] [14 <./Cc1ccccc1.png>] [15] [16] [17] [18] [19] [20] [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 1836--1839 []\T1/qtm/m/n/10 An-other op-tion for Com-pute2DCoords al-lows you to gen-er-at e 2D de-pic-tions for molecules that Underfull \hbox (badness 10000) in paragraph at lines 1836--1839 \T1/qtm/m/n/10 closely mimic 3D con-form-ers. This is avail-able us-ing the fun c-tion \T1/txtt/m/n/10 rdkit.Chem.AllChem. Underfull \hbox (badness 10000) in paragraph at lines 1861--1867 []\T1/qtm/m/n/10 More fine-grained con-trol can be ob-tained us-ing the core fu nc-tion \T1/txtt/m/n/10 rdkit.Chem.rdDepictor. 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[85 <./picture_9.png (PNG copy)>] [86 <./picture_8.png> <./picture_7.png (PNG copy)>] [87 <./picture_10.png> <./picture_12.png>] [88 <./picture_11.png>] [89] [90] [91] [92] [93] [94] Underfull \hbox (badness 10000) in paragraph at lines 7298--7303 []\T1/qtm/m/n/10 Hence, a sin-gle change to SMARTS in-ter-pre-ta-tion, for ex-p res-sions of the form: [95] [96] [97 <./parastereo_2.png> <./parastereo_1.png> <./potential_stereo_double_bond1. png> <./potential_stereo_double_bond2.png>] [98 <./potential_stereo_double_bond3.png>] [99] [100 <./nontetstereo_sp1.png> <./nontetstereo_sp2.png> <./nontetstereo_sp3.png> <./nontetstereo_sp4.png>] [101 <./nontetstereo_tb2.png> <./nontetstereo_tb1.png>] [102 <./nontetstereo_oh 2.png> <./nontetstereo_oh1.png>] Underfull \hbox (badness 10000) in paragraph at lines 9413--9415 []\T1/qtm/m/n/10 The clas-sic ex-am-ple of this is cis-platin - \T1/txtt/m/n/10 Cl[Pt@SP1](Cl)(<[][NH3])<[][NH3] \T1/qtm/m/n/10 - vs trans-platin - [103 <./nontetstereo_ex1.png> <./nontetstereo_ex2.png> <./nontetstereo_missing1 .png>] [104] [105] [106] [107] [108] [109] [110] [111 <./picture_10.jpg>] Overfull \vbox (2.86082pt too high) detected at line 10236 [112] [113 <./ary_group.png>] [114] [115] Underfull \hbox (badness 10000) in paragraph at lines 10871--10873 \T1/qtm/m/n/10 Here's the rd-kitj-son rep-re-sen-ta-tion of the stereo groups f rom the molecule [116] Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 _Chi-ral-i-ty-Pos-si- Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 _Re-ac-tion-De- Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 mo-lAtomMap- Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 molFileIn-ver- Underfull \hbox (badness 10000) in paragraph at lines 11109--11109 []\T1/qtm/m/n/10 mol-Rxn-Com-po- [117] [118] Underfull \hbox (badness 10000) in paragraph at lines 11271--11276 []\T1/qtm/m/n/10 By de-fault the \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles.SDMolSup plier \T1/qtm/m/n/10 and \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles. 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[123] [124 <./EnhancedStereoSSS_molA.png> <./EnhancedStereoSSS_molB.png> <./EnhancedS tereoSSS_molC.png> <./EnhancedStereoSSS_molD.png> <./EnhancedStereoSSS_molE.png > <./EnhancedStereoSSS_molF.png> <./EnhancedStereoSSS_molG.png>] [125] [126 <./atrop_example1.png> <./atrop_example2.png> <./atrop_example3.png>] [127 <./atrop_representation1.png>] [128 <./atrop_example4.png>] [129 <./atrop_example5.png> <./atrop_representation2.png>] [130 <./query_bonds.png>] [131 <./query_bonds.2.png> <./query_atoms.png>] [132] [133] Underfull \hbox (badness 10000) in paragraph at lines 12578--12588 []\T1/txtt/m/n/10 allowNontetrahedralChirality\T1/qtm/m/n/10 : when this is \T1 /txtt/m/n/10 true \T1/qtm/m/n/10 non-tetrahedral chi-ral-ity will be per- Underfull \hbox (badness 10000) in paragraph at lines 12578--12588 \T1/qtm/m/n/10 ceived from 3D co-or-di-nates. The de-fault value is \T1/txtt/m/ n/10 true \T1/qtm/m/n/10 un-less the en-vi-ron-ment vari- Underfull \hbox (badness 10000) in paragraph at lines 12578--12588 \T1/qtm/m/n/10 able \T1/txtt/m/n/10 RDK_ENABLE_NONTETRAHEDRAL_STEREO \T1/qtm/m/ n/10 is set to \T1/txtt/m/n/10 "0"\T1/qtm/m/n/10 . Can set/checked from Underfull \hbox (badness 10000) in paragraph at lines 12578--12588 \T1/qtm/m/n/10 C++ us-ing the func-tions \T1/txtt/m/n/10 RDKit::Chirality::setA llowNontetrahedralChirality() \T1/qtm/m/n/10 / Underfull \hbox (badness 10000) in paragraph at lines 12578--12588 \T1/txtt/m/n/10 RDKit::Chirality::getAllowNontetrahedralChirality() \T1/qtm/m/n /10 or from Python us-ing the func-tions Underfull \hbox (badness 10000) in paragraph at lines 12590--12600 []\T1/txtt/m/n/10 useLegacyStereoPerception\T1/qtm/m/n/10 : when this is \T1/tx tt/m/n/10 true \T1/qtm/m/n/10 the legacy im-ple-men-ta-tion for per- Underfull \hbox (badness 10000) in paragraph at lines 12590--12600 \T1/qtm/m/n/10 ceiv-ing stere-o-chem-istry will be used. The de-fault value is \T1/txtt/m/n/10 true \T1/qtm/m/n/10 un-less the en-vi-ron- Underfull \hbox (badness 10000) in paragraph at lines 12590--12600 \T1/qtm/m/n/10 ment vari-able \T1/txtt/m/n/10 RDK_USE_LEGACY_STEREO_PERCEPTION \T1/qtm/m/n/10 is set to \T1/txtt/m/n/10 "0"\T1/qtm/m/n/10 . Can set/checked Underfull \hbox (badness 10000) in paragraph at lines 12590--12600 \T1/qtm/m/n/10 from C++ us-ing the func-tions \T1/txtt/m/n/10 RDKit::Chirality: :setUseLegacyStereoPerception() \T1/qtm/m/n/10 / [134] [135] [136] Chapter 5. [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] Underfull \vbox (badness 1226) detected at line 13540 [148] [149] [150] Chapter 6. [151] [152 <./RDKitCB_0_im0.png> <./RDKitCB_0_im1.png>] [153 <./RDKitCB_0_im2.png> <./RDKitCB_40_im0.png>] [154 <./RDKitCB_40_im1.png> <./RDKitCB_23_im0.png>] [155 <./RDKitCB_23_im1.png> <./RDKitCB_32_im0.png>] [156 <./RDKitCB_32_im1.png> <./RDKitCB_1_im0.png (PNG copy)>] [157 <./RDKitCB_1_im1.png (PNG copy)> <./RDKitCB_1_im2.png (PNG copy)>] [158 <./RDKitCB_1_im3.png (PNG copy)> <./RDKitCB_2_im0.png>] [159 <./RDKitCB_2_im1.png> <./RDKitCB_36_im0.png>] [160 <./RDKitCB_36_im1.png>] [161 <./RDKitCB_38_im0.png>] [162 <./RDKitCB_39_im0.png (PNG copy)>] [163 <./RDKitCB_17_im0.png> <./RDKitCB_17_im1.png>] [164 <./RDKitCB_34_im0.png> <./RDKitCB_34_im1.png> <./RDKitCB_34_im2.png>] [165] Overfull \hbox (396.49246pt too wide) in paragraph at lines 14208--14208 []\T1/txtt/m/n/10 CC(C)C(O)C1C(=O)NC(CC)C(=O)N(C)CC(=O)N(C)C(CC(C)C)C(=O)NC(C(C )C)C(=O)N(C)C(CC(C)C)C(=O)NC(C)C(=O)NC(C)C(=O)N(C)C(CC(C)C)C(=O)N(C)C(CC(C)C)C( =O)N(C)C(C(C)C)C(=O)N1C[][] [166 <./RDKitCB_37_im0.png>] Overfull \hbox (396.49246pt too wide) in paragraph at lines 14237--14237 []\T1/txtt/m/n/10 CC(C)C(O)C1C(=O)NC(CC)C(=O)N(C)CC(=O)N(C)C(CC(C)C)C(=O)NC(C(C )C)C(=O)N(C)C(CC(C)C)C(=O)NC(C)C(=O)NC(C)C(=O)N(C)C(CC(C)C)C(=O)N(C)C(CC(C)C)C( =O)N(C)C(C(C)C)C(=O)N1C[][] [167 <./RDKitCB_37_im1.png>] [168 <./RDKitCB_37_im2.png>] [169 <./RDKitCB_35_im0.png>] [170] [171 <./RDKitCB_3_im0.png> <./RDKitCB_8_im0.png>] [172] [173 <./RDKitCB_30_im0.png>] [174 <./RDKitCB_30_im1.png>] [175 <./RDKitCB_7_im0.png> <./RDKitCB_7_im1.png>] [176 <./RDKitCB_7_im2.png (PNG copy)> <./RDKitCB_7_im3.png> <./RDKitCB_7_im4.pn g>] [177 <./RDKitCB_7_im5.png> <./RDKitCB_7_im6.png (PNG copy)>] [178] [179] [180 <./RDKitCB_29_im0.png (PNG copy)>] Underfull \vbox (badness 1043) detected at line 14891 [181 <./RDKitCB_33_im0.png (PNG copy)>] Overfull \vbox (0.99814pt too high) detected at line 14926 [182 <./RDKitCB_33_im1.png (PNG copy)>] [183 <./RDKitCB_33_im2.png (PNG copy)>] Overfull \hbox (490.99219pt too wide) in paragraph at lines 14992--14992 []\T1/txtt/m/n/10 "[][]CC[C@@H]1[C@@]([C@@H]([C@H](C(=O)[C@@H](C[C@@]([C@@H]([C @H]([C@@H]([C@H](C(=O)O1)C)O[C@H]2C[C@@]([C@H]([C@@H](O2)C)O)(C)OC)C)O[C@H]3[C@ @H]([C@H](C[C@H](O3)C)N(C)C)O)(C)O)C)C)O)(C)O[][] [184 <./RDKitCB_13_im0.png>] [185 <./RDKitCB_13_im1.png>] [186] [187 <./RDKitCB_20_im0.png>] [188 <./RDKitCB_21_im0.png>] [189 <./RDKitCB_21_im1.png>] [190 <./RDKitCB_21_im2.png (PNG copy)> <./RDKitCB_21_im3.png>] [191 <./RDKitCB_21_im4.png>] [192 <./RDKitCB_21_im5.png (PNG copy)>] [193 <./RDKitCB_22_im0.png>] [194 <./RDKitCB_22_im1.png>] [195 <./RDKitCB_6_im0.png (PNG copy)>] [196 <./RDKitCB_6_im1.png (PNG copy)> <./RDKitCB_6_im2.png (PNG copy)>] [197] [198 <./RDKitCB_15_im0.png> <./RDKitCB_15_im1.png>] [199] [200] [201] [202 <./RDKitCB_19_im0.png>] [203] [204] [205 <./RDKitCB_28_im0.png (PNG copy)> <./RDKitCB_28_im1.png (PNG copy)>] [206] [207] [208] Chapter 7. [209] [210] [211] [212] Overfull \hbox (1052.74055pt too wide) in paragraph at lines 16538--16538 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@@H]2CCCN2C(=O)[C@@H]2CCCN2C(=O)[C@H ]([C@@H](C)CC)NC(=O)[C@H](CO)NC(=O)[C@H](C)NC(=O)[C@H]([C@H](C)O)NC(=O)[C@@H]2C SSC[C@H](NC1=O)C(=O)N[C@@H](Cc1cnc[nH]1)C(=O)N[C@H](Cc1ccccc1)C(=O)N[C@@H](CCCN C(=N)N)C(=O)N[C@@H](Cc1c[nH]c3ccccc13)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N2| Overfull \hbox (149.74318pt too wide) in paragraph at lines 16540--16540 []\T1/txtt/m/n/10 CN1C(=O)[C@H](CCCNC(=N)N)NC(=O)[C@@H](Cc2ccc(O)cc2)NC(=O)[C@@ H]2CCCN2C(=O)[C@H](Cc2ccc3ccccc3c2)NC(=O)[C@@H]1CC(=O)O| Overfull \hbox (97.24333pt too wide) in paragraph at lines 16541--16541 []\T1/txtt/m/n/10 NCCCC[C@H](NC(=O)[C@H](Cc1ccc(OP(=O)(O)O)cc1)NC(=O)Cc1ccccc1) C(=O)N1CCC[C@H]1C(=O)N[C@@H](Cc1ccccc1)C(N)=O| Overfull \hbox (643.24174pt too wide) in paragraph at lines 16542--16542 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCNC(=O)CN(CC(=O)NC(C)(C)C(=O)N[C@@H](Cc1ccccc1 )C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N1CCC[ C@H]1C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](CC(N)=O)C(N)=O)C(=O)c1cccnc1| Overfull \hbox (464.74226pt too wide) in paragraph at lines 16543--16543 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCN(CCCCCCCCCCCCCCCC)CCCCCC(=O)NC(C)(C)C(=O)NC( Cc1ccccc1)C(=O)NC(CC(C)C)C(=O)NC(Cc1ccccc1)C(=O)NC(CCCNC(=N)N)C(=O)N1CCCC1C(=O) NC(CCCNC(=N)N)C(=O)NC(CC(N)=O)C(N)=O| Overfull \hbox (359.74257pt too wide) in paragraph at lines 16544--16544 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CCSC)NC1=O| Overfull \hbox (370.24254pt too wide) in paragraph at lines 16545--16545 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CC[S+](C)[O- Overfull \hbox (422.74239pt too wide) in paragraph at lines 16546--16546 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H](Cc 2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CCSC)NC(=O)[C@H](CC( C)C)NC(=O)[C@H](CC[S+](C)[O- Overfull \hbox (249.49289pt too wide) in paragraph at lines 16547--16547 []\T1/txtt/m/n/10 ])NC(=O)[C@H](C(C)C)NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H] (Cc2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CC[S+](C)[O- Overfull \vbox (2.3893pt too high) detected at line 16549 [213] Overfull \hbox (1052.74055pt too wide) in paragraph at lines 16561--16561 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@@H]2CCCN2C(=O)[C@@H]2CCCN2C(=O)[C@H ]([C@@H](C)CC)NC(=O)[C@H](CO)NC(=O)[C@H](C)NC(=O)[C@H]([C@H](C)O)NC(=O)[C@@H]2C SSC[C@H](NC1=O)C(=O)N[C@@H](Cc1cnc[nH]1)C(=O)N[C@H](Cc1ccccc1)C(=O)N[C@@H](CCCN C(=N)N)C(=O)N[C@@H](Cc1c[nH]c3ccccc13)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N2| Overfull \hbox (149.74318pt too wide) in paragraph at lines 16563--16563 []\T1/txtt/m/n/10 CN1C(=O)[C@H](CCCNC(=N)N)NC(=O)[C@@H](Cc2ccc(O)cc2)NC(=O)[C@@ H]2CCCN2C(=O)[C@H](Cc2ccc3ccccc3c2)NC(=O)[C@@H]1CC(=O)O| Overfull \hbox (97.24333pt too wide) in paragraph at lines 16564--16564 []\T1/txtt/m/n/10 NCCCC[C@H](NC(=O)[C@H](Cc1ccc(OP(=O)(O)O)cc1)NC(=O)Cc1ccccc1) C(=O)N1CCC[C@H]1C(=O)N[C@@H](Cc1ccccc1)C(N)=O| Overfull \hbox (643.24174pt too wide) in paragraph at lines 16565--16565 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCNC(=O)CN(CC(=O)NC(C)(C)C(=O)N[C@@H](Cc1ccccc1 )C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N1CCC[ C@H]1C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](CC(N)=O)C(N)=O)C(=O)c1cccnc1| Overfull \hbox (359.74257pt too wide) in paragraph at lines 16566--16566 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CCSC)NC1=O| Overfull \hbox (370.24254pt too wide) in paragraph at lines 16567--16567 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CC[S+](C)[O- Overfull \hbox (422.74239pt too wide) in paragraph at lines 16568--16568 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H](Cc 2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CCSC)NC(=O)[C@H](CC( C)C)NC(=O)[C@H](CC[S+](C)[O- Overfull \hbox (249.49289pt too wide) in paragraph at lines 16569--16569 []\T1/txtt/m/n/10 ])NC(=O)[C@H](C(C)C)NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H] (Cc2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CC[S+](C)[O- Overfull \hbox (522.4921pt too wide) in paragraph at lines 16570--16570 []\T1/txtt/m/n/10 CC[C@H](C)[C@H](N)C(=O)N[C@H](C(=O)N[C@@H](CC(C)C)C(=O)N[C@H] (C(=O)N1CCC[C@H]1C(=O)N1CCC[C@H]1C(=O)N[C@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CC(C )C)C(=O)O)Cc1ccccc1)Cc1ccccc1)C(C)C)[C@@H](C)CC| [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] Chapter 8. [229] [230] [231] Underfull \hbox (badness 10000) in paragraph at lines 17791--17795 \T1/qtm/m/n/10 Un-charger::uncharge() will now neu-tral-ize \T1/txtt/m/n/10 [Cl ,Br,I][O[]], [Cl,Br,I](=O)[O[]], [Cl, Underfull \hbox (badness 10000) in paragraph at lines 17791--17795 \T1/txtt/m/n/10 Br,I](=O)(=O)[O[]], [Cl,Br,I](=O)(=O)(=O)[O[]], [O[]]N=N[O[]], [N,P](=O)[O[]], Underfull \hbox (badness 10000) in paragraph at lines 17791--17795 \T1/txtt/m/n/10 [N+](=O)([O[]])[O[]], P(=O)([O[]])[O[]], P(=O)([O[]])([O[]])[O[ ]], S([O[]])[O[]], S(=O)([O[]])[O[]], [232] [233] [234] Chapter 9. [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] Chapter 10. [247] [248] [249] Underfull \hbox (badness 10000) in paragraph at lines 19693--19697 \T1/qtm/m/n/10 Groups of molecules are read us-ing a Sup-plier (for ex-am-ple, an \T1/txtt/m/n/10 RDKit::SDMolSupplier \T1/qtm/m/n/10 or an [250] [251] [252] [253] [254] Overfull \vbox (0.8796pt too high) detected at line 20130 [255] [256] Underfull \hbox (badness 6691) in paragraph at lines 20233--20235 []\T1/qtm/m/n/10 The \T1/txtt/m/n/10 auto\TS1/txtt/m/n/10 ' \T1/txtt/m/n/10 key word here is hiding the fact that \T1/qtm/m/n/10 get-Bond-Be-tweenAtoms\T1/txtt /m/n/10 returns the index of the [257] [258] [259] [260] [261] [262] [263] [264] [265] [266] [267] [268] Overfull \vbox (1.8739pt too high) detected at line 21250 [269] [270] [271] [272] Chapter 11. [273] [274] Chapter 12. (./RDKit.ind) [275] (./RDKit.aux) ) (see the transcript file for additional information) Output written on RDKit.pdf (279 pages, 2962408 bytes). Transcript written on RDKit.log. Latexmk: Getting log file 'RDKit.log' Latexmk: Examining 'RDKit.fls' Latexmk: Examining 'RDKit.log' Latexmk: Index file 'RDKit.idx' was written Latexmk: Log file says output to 'RDKit.pdf' Have index file 'RDKit.idx', RDKit.ind RDKit Latexmk: All targets (RDKit.pdf) are up-to-date make[3]: Leaving directory '/build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex' pdflatex finished; the PDF files are in _build/latex. make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.6/Docs/Book' make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/rdkit-202409.6' cp -r rdkit obj-*/ find /build/reproducible-path/rdkit-202409.6 -name rdchem.so /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so PYTHONPATH=/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/:/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib:" dh_auto_test cd obj-aarch64-linux-gnu && make -j12 test ARGS\+=--verbose ARGS\+=-j12 make[2]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j12 UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/DartConfiguration.tcl Add coverage exclude regular expressions. UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/rdkit-202409.6/obj-aarch64-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 Connected to MAKE jobserver test 1 Start 1: testCoordGen 1: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/CoordGen/testCoordGen 1: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/CoordGen 1: Test timeout computed to be: 1500 test 2 Start 2: pyCoordGen 2: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/External/CoordGen/Wrap/testCoordGen.py" 2: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/CoordGen/Wrap 2: Test timeout computed to be: 1500 test 3 Start 3: testDict 3: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral/testDict 3: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral 3: Test timeout computed to be: 1500 test 4 Start 4: testRDValue 4: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral/testRDValue 4: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral 4: Test timeout computed to be: 1500 test 5 Start 5: testConcurrentQueue 5: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral/testConcurrentQueue 5: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral 5: Test timeout computed to be: 1500 test 6 Start 6: dictTestsCatch 6: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral/dictTestsCatch 6: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral 6: Test timeout computed to be: 1500 test 7 Start 7: logTestsCatch 7: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral/logTestsCatch 7: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral 7: Test timeout computed to be: 1500 test 8 Start 8: testDataStructs 8: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/testDataStructs 8: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs 8: Test timeout computed to be: 1500 test 9 Start 9: testFPB 9: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/testFPB 9: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs 9: Test timeout computed to be: 1500 test 10 Start 10: testMultiFPB 10: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/testMultiFPB 10: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs 10: Test timeout computed to be: 1500 test 11 Start 11: catchDataStructs 11: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/catchDataStructs 11: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs 11: Test timeout computed to be: 1500 test 12 Start 12: pyBV 12: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/testBV.py" 12: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap 12: Test timeout computed to be: 1500 3: [15:23:02] Testing Github940: property dictionaries leaking memory 3: [15:23:02] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect 3: dict get int vect 3: static boost any:0.000271 s 3: dynamic boost any:0.001034 s 3: static RDAny:0.000124 s 3: dynamic RDAny:0.000974 s 3: static RDValue:0 s 3: dynamic RDValue:0.000155 s 3: deleted! 3: [15:23:02] ------------------------------------- 3: [15:23:02] Testing String Pickle Roundtrips. 3: [15:23:02] done 3: [15:23:02] ------------------------------------- 3: [15:23:02] Testing conversion of vect to string. 3: [15:23:02] done 3: [15:23:02] ------------------------------------- 3: [15:23:02] Testing returning const references. 3: [15:23:02] any cast 3: [15:23:02] done: 0.000815 300000 3: [15:23:02] copy 3: [15:23:02] done: 0.000853 300000 3: [15:23:02] ref 3: [15:23:02] done: 0.000801 300000 3: [15:23:02] dict 3: [15:23:02] done: 0.001956 300000 3: [15:23:02] ref with hasVal 3: [15:23:02] done: 0.001306 300000 3: [15:23:02] done 3: [15:23:02] ------------------------------------- 3: [15:23:02] Testing dict update. 3: [15:23:02] done 3: deleted! 3: deleted! 3: deleted! 3: deleted! 3: deleted! 3: deleted! 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: [15:23:02] 5: ----------------------------------------- 5: [15:23:02] Finished: testPushAndPop() 5: [15:23:02] 5: ----------------------------------------- 5: [15:23:02] 5: ----------------------------------------- 8: [15:23:02] pass 8: [15:23:02] v3 4 8: [15:23:02] v4 5 8: [15:23:02] SPARSE ----------------------------------- 8: [15:23:02] Set 10: 0 8: [15:23:02] Set 11: 0 8: [15:23:02] Set 14: 0 8: [15:23:02] Set 10: 1 8: [15:23:02] Get 14: 1 8: [15:23:02] Num: 20 8: [15:23:02] NumOn: 3 8: [15:23:02] NumOff: 17 8: 10, 11, 14, 8: [15:23:02] t2[19]: 0 8: [15:23:02] t2[14]: 1 8: [15:23:02] t2[19]: 0 8: [15:23:02] t2[14]: 0 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 1/235 Test #3: testDict ............................... Passed 0.26 sec 2/235 Test #4: testRDValue ............................ Passed 0.28 sec 8: [15:23:02] Explicit ---------------------------------- 8: [15:23:02] Set 10: 0 8: [15:23:02] Set 11: 0 8: [15:23:02] Set 14: 0 8: [15:23:02] Set 10: 1 8: [15:23:02] Get 14: 1 8: [15:23:02] Num: 20 8: [15:23:02] NumOn: 3 8: [15:23:02] NumOff: 17 8: 10, 11, 14, 8: [15:23:02] t2[19]: 0 8: [15:23:02] t2[14]: 1 8: [15:23:02] t2[19]: 0 8: [15:23:02] t2[14]: 0 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: [15:23:02] Done 8: [15:23:02] Test DiscreteValue Vectors 1 ---------------------------- test 13 Start 13: pyDiscreteValueVect 13: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/testDiscreteValueVect.py" 13: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap 13: Test timeout computed to be: 1500 test 14 Start 14: pyRealValueVect 14: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/testRealValueVect.py" 14: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap 14: Test timeout computed to be: 1500 8: [15:23:02] Expected failure: Value out of range 8: [15:23:02] Expected failure: Value out of range 8: [15:23:02] Expected failure: Value out of range 8: [15:23:02] Expected failure: Value out of range 8: [15:23:02] Expected failure: Value out of range 8: [15:23:02] Test DiscreteValue Vectors 2 ------------------------------ 8: [15:23:02] Test DiscreteValue Vectors 3 --------------------------- 8: [15:23:02] Test DiscreteValue Operations ----------------------------- 8: [15:23:02] Test DiscreteValue Operations 2 -------------------------- 8: [15:23:02] Test SparseIntVect ------------------------------------ 8: [15:23:02] Test SparseIntVect Serialization -------------------------- 8: [15:23:02] Test BitVect Serialization ------------------------------- 8: [15:23:02] Test BitVect to FPS ------------------------------- 8: [15:23:02] Test BitVect to binary string ------------------------------- 8: [15:23:02] Test Similarity Measures BitVect ------------------------------- 8: [15:23:02] Test Similarity Measures SparseBitVect ------------------------------- 8: [15:23:02] Test BitVect with all ones ------------------------------- 8: [15:23:02] Test Explicit BitVects: Concatenation Operation ------------------------------- 8: [15:23:02] Test bitmap operations ------------------------------- 8: [15:23:02] Test bitmaps as properties ------------------------------- 8: [15:23:02] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- 3/235 Test #9: testFPB ................................ Passed 0.23 sec test 15 Start 15: pySparseIntVect 15: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/testSparseIntVect.py" 15: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap 15: Test timeout computed to be: 1500 8: [15:23:02] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- 8: [15:23:02] Test RealValue Vectors 2: L1Norm ------------------------------- 8: [15:23:02] Test RealValue Vectors 3: Pickles ------------------------------- 8: [15:23:02] Test RealValue Vectors 4: Vector Operations ------------------------------- 4/235 Test #8: testDataStructs ........................ Passed 0.27 sec test 16 Start 16: pyFPB 16: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/testFPB.py" 16: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap 16: Test timeout computed to be: 1500 7: [15:23:02] should not be silent 7: [15:23:02] should not be silent 7: Randomness seeded to: 3461035271 7: [15:23:02] should not be silent 7: [15:23:02] should not be silent 7: [15:23:02] should not be silent 7: [15:23:02] should not be silent 7: [15:23:02] should not be silent 7: [15:23:02] should not be silent 7: [15:23:02] should not be silent 7: [15:23:02] should not be silent 7: =============================================================================== 7: All tests passed (26 assertions in 3 test cases) 7: 5/235 Test #7: logTestsCatch .......................... Passed 0.37 sec test 17 Start 17: testTransforms 17: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/testTransforms 17: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry 17: Test timeout computed to be: 1500 6/235 Test #10: testMultiFPB ........................... Passed 0.27 sec test 18 Start 18: testGrid 18: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/testGrid 18: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry 18: Test timeout computed to be: 1500 6: Randomness seeded to: 2382420890 6: =============================================================================== 6: All tests passed (32 assertions in 2 test cases) 6: 17: **************************************** 17: testPointND 17: **************************************** 17: testPointOps3D 17: **************************************** 17: testPointOps2D 17: **************************************** 17: test12D 17: ref1: 1.48105 2.06261 ref2: 2.68915 0.680788 17: pt1: 2.8714 2.01527 pt2: 0.283449 1.1894 17: **************************************** 17: test23D 17: **************************************** 17: test3MatMultiply 17: Pt1: 1 0 0 Pt2: 2 0 0 17: -Pt1: -1 -0 -0 17: tp1: 0 0 0 tp2: 0 0 0 17: tp1: 0 0 0 tp2: 0 0 0 17: tp1: 0 0 3 tp2: 0 0 3 17: npt1: 0 0 3 npt2: 0 0 4 17: Pt1: 0 0 3 Pt2: 6.12323e-17 0 4 17: **************************************** 17: testFromQuaternion 17: **************************************** 7/235 Test #17: testTransforms ......................... Passed 0.09 sec test 19 Start 19: testRealValueGrid 19: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/testRealValueGrid 19: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry 19: Test timeout computed to be: 1500 18: *********************************************************** 18: Testing Grid 18: --------------------------------- 18: testUniformGrid1 18: 18: --------------------------------- 18: testUniformGrid2 18: 18: --------------------------------- 18: testUniformGridPickling 18: 18: --------------------------------- 18: testGridOps 18: 18: --------------------------------- 18: testUniformGridIndexing 18: 8/235 Test #6: dictTestsCatch ......................... Passed 0.49 sec test 20 Start 20: geometryTestsCatch 20: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/geometryTestsCatch 20: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry 20: Test timeout computed to be: 1500 9/235 Test #18: testGrid ............................... Passed 0.10 sec test 21 Start 21: testPyGeometry 21: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap/testGeometry.py" 21: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/Wrap 21: Test timeout computed to be: 1500 19: *********************************************************** 19: Testing RealValueGrid3D 19: --------------------------------- 19: test1UniformRealValueGrid3D 19: 19: --------------------------------- 19: test2UniformRealValueGrid3DPickling 19: 19: --------------------------------- 19: test3UniformRealValueGrid3DIndexing 19: 19: --------------------------------- 19: test4UniformRealValueGrid3DOps 19: 10/235 Test #19: testRealValueGrid ...................... Passed 0.11 sec test 22 Start 22: testMatrices 22: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/testMatrices 22: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics 22: Test timeout computed to be: 1500 11: Randomness seeded to: 3456364653 11: =============================================================================== 11: All tests passed (3 assertions in 1 test case) 11: 11/235 Test #11: catchDataStructs ....................... Passed 0.44 sec test 23 Start 23: testConrec 23: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/testConrec 23: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics 23: Test timeout computed to be: 1500 22: [15:23:03] ----------------------------------------- 22: [15:23:03] Testing RDNumerics: vectors and matrices Code 22: [15:23:03] --------------------------------------- 22: [15:23:03] test1Vector 22: [15:23:03] --------------------------------------- 22: [15:23:03] test2Matrix 22: [15:23:03] --------------------------------------- 22: [15:23:03] test3SquareMatrix 22: [15:23:03] --------------------------------------- 22: [15:23:03] test4SymmMatrix 12/235 Test #22: testMatrices ........................... Passed 0.07 sec test 24 Start 24: testAlignment 24: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment/testAlignment 24: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment 24: Test timeout computed to be: 1500 24: ----------------------------------------- 24: Testing Alignment Code 24: --------------------------------------- 24: testBasic 24: --------------------------------------- 24: testTriangle 24: --------------------------------------- 24: testFourPts 24: --------------------------------------- 24: testReflection 24: --------------------------------------- 13/235 Test #24: testAlignment .......................... Passed 0.08 sec test 25 Start 25: pyAlignment 25: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment/Wrap/testAlignment.py" 25: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap 25: Test timeout computed to be: 1500 20: Randomness seeded to: 1929393727 20: =============================================================================== 20: All tests passed (50 assertions in 5 test cases) 20: 14/235 Test #20: geometryTestsCatch ..................... Passed 0.40 sec test 26 Start 26: testOptimizer 26: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/testOptimizer 26: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer 26: Test timeout computed to be: 1500 26: ------------------------------------- 26: Testing linear search. 26: done 26: ------------------------------------- 26: Testing BFGS optimization. 26: done 15/235 Test #26: testOptimizer .......................... Passed 0.04 sec test 27 Start 27: ForceFieldsCatch 27: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/ForceFieldsCatch 27: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField 27: Test timeout computed to be: 1500 23: Randomness seeded to: 1892244272 23: =============================================================================== 23: All tests passed (76 assertions in 3 test cases) 23: 16/235 Test #23: testConrec ............................. Passed 0.45 sec test 28 Start 28: testUFFForceField 28: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/UFF/testUFFForceField 28: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/UFF 28: Test timeout computed to be: 1500 28: ------------------------------------- 28: Unit tests for force field basics. 28: done 28: ------------------------------------- 28: Unit tests for basics of UFF bond-stretch terms. 28: done 28: ------------------------------------- 28: Unit tests for UFF bond-stretch terms. 28: done 28: ------------------------------------- 28: Unit tests for basics of UFF angle terms. 28: done 28: ------------------------------------- 28: Unit tests for UFF angle-bend terms. 28: theta = 3.14159; theta0 = 3.14159 28: theta = 2.094395, param1.theta0 = 2.094395 28: done 28: ------------------------------------- 28: Test Simple UFF molecule optimizations. 28: done 28: ------------------------------------- 28: Unit tests for UFF nonbonded terms. 28: done 28: ------------------------------------- 28: Test UFF torsional terms. 28: done 28: ------------------------------------- 28: Test UFF Parameter objects 28: ------------------------------------- 28: Test Simple UFF molecule optimization, part 2. 28: done 28: ------------------------------------- 28: Test UFF Torsion Conflicts. 28: C 0.4783 -0.7477 -0.0753 28: C -0.5465 -0.0176 0.3519 28: C -0.5114 1.4472 0.0870 28: H -1.5201 -0.4838 0.2485 28: H 0.4696 1.8363 0.3367 28: O -1.2618 1.9423 0.6934 28: F -0.7163 1.6298 -0.9622 28: done 28: ------------------------------------- 28: Unit tests for UFF distance constraint terms. 28: done 28: ------------------------------------- 28: Unit tests for all UFF constraint terms. 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: 27: Randomness seeded to: 536328395 27: =============================================================================== 27: All tests passed (20 assertions in 2 test cases) 27: 1: templated 1: RDKit 2D 1: 1: 7 7 0 0 0 0 0 0 0 0999 V2000 1: 0.6824 0.1850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.1850 -0.6824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.6824 -0.1850 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1850 0.6824 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 2 6 1 0 1: 6 7 1 0 1: 7 1 1 0 1: M END 1: 1: core 1: RDKit 2D 1: 1: 10 10 0 0 0 0 0 0 0 0999 V2000 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 1 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 12 12 0 0 0 0 0 0 0 0999 V2000 1: 0.2846 -0.7516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2790 -1.7516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5898 -2.2466 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4530 -1.7418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4476 -0.7418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5788 -0.2468 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5732 0.7532 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2956 1.2484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3012 2.2482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.1700 2.7434 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.1590 0.7434 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.1534 -0.2564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 8 11 1 0 1: 11 12 1 0 1: 12 1 1 0 1: M END 1: 1: templated 1: RDKit 2D 1: 1: 12 12 0 0 0 0 0 0 0 0999 V2000 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 8 11 1 0 1: 11 12 1 0 1: 12 1 1 0 1: M END 1: 1: core 1: RDKit 2D 1: 1: 10 10 0 0 0 0 0 0 0 0999 V2000 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 1 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 16 16 0 0 0 0 0 0 0 0999 V2000 1: 1.7868 0.7799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.6532 1.2791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.5187 0.7785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.5180 -0.2215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.6515 -0.7209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.7860 -0.2201 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.9195 -0.7195 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0539 -0.2189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8124 -0.7181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.6780 -0.2175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.5445 -0.7167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.4101 -0.2161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.2764 -0.7153 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.1421 -0.2147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0547 0.7811 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.9211 1.2805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 11 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 8 15 1 0 1: 15 16 1 0 1: 16 1 1 0 1: M END 1: 1: templated 1: RDKit 2D 1: 1: 16 16 0 0 0 0 0 0 0 0999 V2000 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 11 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 8 15 1 0 1: 15 16 1 0 1: 16 1 1 0 1: M END 1: 1: core 1: RDKit 2D 1: 1: 9 10 0 0 0 0 0 0 0 0999 V2000 1: 0.6718 -0.9994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5374 -0.4988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5366 0.5012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6702 1.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1954 0.4998 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1946 -0.5002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1454 -0.8098 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.7338 -0.0014 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1466 0.8082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 6 1 1 0 1: 9 5 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 19 21 0 0 0 0 0 0 0 0999 V2000 1: -0.5657 -0.9286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4321 -0.4294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.2977 -0.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.2969 -1.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.1625 -2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4329 0.5708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5673 1.0714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5681 2.0714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2975 2.5720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2975 2.5728 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.7969 3.4386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2991 0.5720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2999 -0.4278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2513 -0.7362 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5609 -1.6870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5393 -1.8942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8923 -2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.8381 0.0734 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2499 0.8820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 2 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 7 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 14 15 1 0 1: 15 16 1 0 1: 15 17 1 0 1: 14 18 1 0 1: 18 19 1 0 1: 13 1 1 0 1: 19 12 1 0 1: 11 9 1 0 1: M END 1: 1: templated 1: RDKit 2D 1: 1: 19 21 0 0 0 0 0 0 0 0999 V2000 1: 0.5360 -0.9365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4021 -0.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2680 -0.9366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2680 -1.9366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4020 -2.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4021 0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5360 1.0633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5360 2.0634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.3300 2.5633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3300 2.5633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8300 3.4295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.3300 0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.3300 -0.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2812 -0.7457 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.5900 -1.6966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.9208 -2.4398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.5682 -1.9046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.8686 0.0634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2812 0.8725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 2 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 7 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 14 15 1 0 1: 15 16 1 0 1: 15 17 1 0 1: 14 18 1 0 1: 18 19 1 0 1: 13 1 1 0 1: 19 12 1 0 1: 11 9 1 0 1: M END 1: 1: core 1: RDKit 2D 1: 1: 5 4 0 0 0 0 0 0 0 0999 V2000 1: 1.2134 -0.4976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3464 0.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3444 1.0006 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5186 -0.5010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3856 -0.0028 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 2 4 1 0 1: 4 5 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 7 6 0 0 0 0 0 0 0 0999 V2000 1: -1.7333 -0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8661 -0.0697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8641 0.9303 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0011 -0.5713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8659 -0.0731 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8679 0.9269 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.7309 -0.5749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 2 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 5 7 1 0 1: M END 1: 1: templated 1: RDKit 2D 1: 1: 7 6 0 0 0 0 0 0 0 0999 V2000 1: 1.2227 -0.4921 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: 0.3350 1.0058 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5185 -0.5117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3902 -0.0216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.2506 -0.5314 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4014 0.9784 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: 17/235 Test #27: ForceFieldsCatch ....................... Passed 0.56 sec test 29 Start 29: testMMFFForceField 29: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField 29: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/MMFF 29: Test timeout computed to be: 1500 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: 28: done 28: ------------------------------------- 28: Unit tests for copying UFF ForceFields. 29: ------------------------------------- 29: Official MMFF validation suite. 28: done 28: ------------------------------------- 28: Unit test for UFF butane scan. 16: ......... 16: ---------------------------------------------------------------------- 16: Ran 9 tests in 0.126s 16: 16: OK 13: ...... 13: ---------------------------------------------------------------------- 13: Ran 6 tests in 0.119s 13: 13: OK 14: ...... 14: ---------------------------------------------------------------------- 14: Ran 6 tests in 0.023s 14: 14: OK 15: ......... 15: ---------------------------------------------------------------------- 15: Ran 9 tests in 0.080s 15: 15: OK 25: ..... 25: ---------------------------------------------------------------------- 25: Ran 5 tests in 0.053s 25: 25: OK 25: Testing Alignment Wrapper code: 18/235 Test #13: pyDiscreteValueVect .................... Passed 1.51 sec test 30 Start 30: pyForceFieldConstraints 30: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/ForceField/Wrap/testConstraints.py" 30: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/Wrap 30: Test timeout computed to be: 1500 19/235 Test #16: pyFPB .................................. Passed 1.46 sec test 31 Start 31: testDistGeom 31: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/testDistGeom 31: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom 31: Test timeout computed to be: 1500 20/235 Test #14: pyRealValueVect ........................ Passed 1.58 sec test 32 Start 32: pyDistGeom 32: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DistGeom/Wrap/rough_test.py" 32: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/Wrap 32: Test timeout computed to be: 1500 21/235 Test #25: pyAlignment ............................ Passed 1.12 sec test 33 Start 33: graphmolTest1 33: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 33: Test timeout computed to be: 1500 31: *********************************************************** 31: test1 31: *********************************************************** 31: testIssue216 31: Rows: 4 Columns: 4 31: 0 1 1 1 31: 1 0 1 1 31: 1 1 0 1 31: 1 1 1 0 31: *********************************************************** 31: 22/235 Test #31: testDistGeom ........................... Passed 0.08 sec test 34 Start 34: graphmolcpTest 34: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolcpTest 34: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 34: Test timeout computed to be: 1500 21: .................... 21: ---------------------------------------------------------------------- 21: Ran 20 tests in 0.195s 21: 21: OK 21: Testing Geometry wrapper 23/235 Test #15: pySparseIntVect ........................ Passed 1.58 sec test 35 Start 35: graphmolqueryTest 35: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest 35: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 35: Test timeout computed to be: 1500 28: done 33: Atoms: 33: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 33: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 33: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 33: 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 33: 4 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 33: 5 6 C chg: 0 deg: 1 exp: 3 imp: 1 hyb: 33: 6 6 C chg: 0 deg: 2 exp: 4 imp: 0 hyb: 33: 7 7 N chg: 0 deg: 2 exp: 1 imp: 2 hyb: arom?: 1 query: AtomAtomicNum 33: 8 22 Ti chg: 0 deg: 1 exp: N/A imp: N/A hyb: 33: Bonds: 33: 0 0->1 order: 1 33: 1 1->2 order: 2 33: 2 2->3 order: 1 33: 3 0->4 order: 1 33: 4 5->6 order: 3 33: 5 6->7 order: 1 33: 6 7->8 order: 2 33: [15:23:04] 33: 33: **** 24/235 Test #28: testUFFForceField ...................... Passed 0.86 sec test 36 Start 36: graphmolMolOpsTest 36: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMolOpsTest 36: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 36: Test timeout computed to be: 1500 33: Pre-condition Violation 33: bond already exists 33: Violation occurred on line 499 in file ./Code/GraphMol/RWMol.cpp 33: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) 33: ---------- 33: Stacktrace: 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 33: 3# 0x0000AAAADD78B7A0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 4# 0x0000AAAADD783DDC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 5# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 33: 7# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: 33: [15:23:04] 33: 33: **** 33: Pre-condition Violation 33: bond already exists 33: Violation occurred on line 499 in file ./Code/GraphMol/RWMol.cpp 33: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) 33: ---------- 33: Stacktrace: 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 33: 3# 0x0000AAAADD78B9C0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 4# 0x0000AAAADD783DDC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 5# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 33: 7# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: 33: [15:23:04] 33: 33: **** 33: Pre-condition Violation 33: attempt to add self-bond 33: Violation occurred on line 498 in file ./Code/GraphMol/RWMol.cpp 33: Failed Expression: atomIdx1 != atomIdx2 33: ---------- 33: Stacktrace: 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 33: 3# 0x0000AAAADD78BAB4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 4# 0x0000AAAADD783DDC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 5# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 33: 7# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: 33: [15:23:04] 33: 33: **** 33: Pre-condition Violation 33: bond already exists 33: Violation occurred on line 419 in file ./Code/GraphMol/ROMol.cpp 33: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) 33: ---------- 33: Stacktrace: 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 33: 3# 0x0000AAAADD78BAF4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 4# 0x0000AAAADD783DDC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 5# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 33: 7# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: 33: [15:23:04] 33: 33: **** 33: Pre-condition Violation 33: attempt to add self-bond 33: Violation occurred on line 417 in file ./Code/GraphMol/ROMol.cpp 33: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() 33: ---------- 33: Stacktrace: 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 33: 3# 0x0000AAAADD78BC3C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 4# 0x0000AAAADD783DDC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 5# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 33: 7# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: 33: [15:23:04] Explicit valence for atom # 0 B, 4, is greater than permitted 33: [15:23:04] Explicit valence for atom # 0 B, 4, is greater than permitted 33: [15:23:04] 33: 33: **** 33: Post-condition Violation 33: Element 'Xx' not found 33: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 33: Failed Expression: anum > -1 33: ---------- 33: Stacktrace: 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 3# 0x0000AAAADD7B6868 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 4# 0x0000AAAADD79A358 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 5# 0x0000AAAADD783DE8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 6# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 33: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 33: 8# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: 33: [15:23:04] ------------------------------------- 33: [15:23:04] Test github381: thread-safe initialization of the periodic table 35: [15:23:04] ---------------------- Test1 25/235 Test #21: testPyGeometry ......................... Passed 1.47 sec test 37 Start 37: graphmoltestChirality 37: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestChirality 37: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 37: Test timeout computed to be: 1500 34: 34: 34: 34: COPY 33: [15:23:04] done 33: [15:23:04] ------------------------------------- 33: [15:23:04] Test github1041: Segfault for atom with no owner (expect some warnings) 33: [15:23:04] 33: 33: **** 33: Pre-condition Violation 33: no owner 33: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 33: Failed Expression: dp_mol 33: ---------- 33: Stacktrace: 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 2# 0x0000AAAADD7AAA58 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 3# 0x0000AAAADD783E0C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 4# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 33: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 33: 6# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: 33: [15:23:04] 33: 33: **** 33: Pre-condition Violation 33: no owner 33: Violation occurred on line 187 in file ./Code/GraphMol/Bond.h 33: Failed Expression: dp_mol 33: ---------- 33: Stacktrace: 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 2# 0x0000AAAADD7AAE34 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 3# 0x0000AAAADD783E0C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 4# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 33: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 33: 6# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: 33: [15:23:04] done 33: [15:23:04] ------------------------------------- 33: [15:23:04] Test github1041: Segfault for atom with no owner (expect some warnings) 33: [15:23:04] 33: 33: **** 33: Pre-condition Violation 33: no owner 33: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 33: Failed Expression: dp_mol 33: ---------- 33: Stacktrace: 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 2# 0x0000AAAADD7AAA58 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 3# 0x0000AAAADD783E10 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 4# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 33: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 33: 6# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: 33: [15:23:04] 33: 33: **** 33: Pre-condition Violation 33: no owner 33: Violation occurred on line 187 in file ./Code/GraphMol/Bond.h 33: Failed Expression: dp_mol 33: ---------- 33: Stacktrace: 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 2# 0x0000AAAADD7AAE34 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 3# 0x0000AAAADD783E10 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: 4# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 33: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 33: 6# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: 33: [15:23:04] done 33: [15:23:04] ------------------------------------- 33: [15:23:04] Test github1453: RWMol.clear() should reset the numBonds count. 33: [15:23:04] done 33: [15:23:04] ------------------------------------- 33: [15:23:04] Test range-based for loops. 33: [15:23:04] done 33: [15:23:04] ------------------------------------- 33: [15:23:04] Test github1642: Atom index type is too low for big molecules. 35: [15:23:04] Done! 35: [15:23:04] ---------------------- Test2 35: [15:23:04] Done! 35: [15:23:04] ---------------------- Test3 26/235 Test #34: graphmolcpTest ......................... Passed 0.16 sec test 38 Start 38: graphmoltestPickler 38: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPickler 38: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 38: Test timeout computed to be: 1500 35: [15:23:04] Done! 35: [15:23:04] ---------------------- Test4 35: [15:23:04] Done! 35: [15:23:04] ---------------------- Test5 35: [15:23:04] Done! 35: [15:23:04] Done! 35: [15:23:04] ---------------------- Test issue 2892580 35: [15:23:04] Done! 35: [15:23:04] ---------------------- Test github issue 53: query molecules not matching [R] 35: [15:23:04] Done! 35: [15:23:04] ---------------------- Test queries using qualifiers instead of == 35: [15:23:04] Done! 36: 1 1 2 36: 1 1 1 36: 2 1 0.75 35: [15:23:04] ---------------------- Test Github issue 165: radicals not used in atom-atom matching 35: [15:23:04] Done! 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing String Pickle Roundtrips. 35: [15:23:04] ---------------------- Test extra atom queries 35: [15:23:04] Done! 35: [15:23:04] ---------------------- Test extra bond queries 35: [15:23:04] Done! 35: [15:23:04] ---------------------- Test num heteroatom neighbor queries 35: [15:23:04] Done! 35: [15:23:04] ---------------------- Test atom type queries 35: [15:23:04] Done! 35: [15:23:04] ---------------------- Test Github #2471: dummy atom queries are flagged as complex 35: [15:23:04] Done! 35: [15:23:04] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() 35: [15:23:04] Done! 27/235 Test #35: graphmolqueryTest ...................... Passed 0.15 sec test 39 Start 39: graphmoltestPicklerGlobalSetting 39: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting 39: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 39: Test timeout computed to be: 1500 1: cyclosporine a 1: RDKit 2D 1: 1: 85 85 0 0 0 0 0 0 0 0999 V2000 1: 1.4840 -0.8529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6174 -1.3521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6176 -2.3509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4860 -2.8479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4912 -3.8491 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.3504 -2.3385 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.3352 -1.3311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.1902 -0.7993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.1580 0.1961 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.0642 -1.2607 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.9260 -0.7295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.9144 0.3303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.7766 0.8337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.0008 0.8409 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.8596 1.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.8162 2.2071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2038 1.4219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2560 3.1855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5280 4.2325 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.7128 4.8927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.8530 5.8895 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.7676 4.5077 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0820 5.0835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.9744 4.6151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.8344 5.1337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.9792 3.6203 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.8192 3.0813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.7974 3.5817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.7998 4.5809 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.7790 3.0789 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.8812 2.0705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.1202 1.6015 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.4194 2.0931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.0590 0.6211 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.8626 0.0983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.8096 -0.8961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.6470 -1.4375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.9122 -1.3587 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.8776 -2.3565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9982 -2.8425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1382 -2.3311 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9886 -3.8459 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1202 -4.3461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2526 -3.8491 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6116 -4.3521 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2494 -2.8505 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1228 -5.3475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2584 -5.8507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6092 -5.3541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2624 -6.8511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6018 -7.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5982 -8.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4624 -8.8579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9906 -5.8449 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.8520 -4.3501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.7288 -2.8719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.7098 -3.8701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.6032 -2.3871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.0646 -0.8235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.7362 0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5794 0.0605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5618 -0.9361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -6.4498 0.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.1628 0.1727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.7698 1.6253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5952 2.1745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -6.4896 1.7311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5292 3.1711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.6054 3.6407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.7186 2.0867 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0328 6.0847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.4396 4.6417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.4580 5.6909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.3220 6.1985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5836 6.2065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2682 3.0557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.6630 2.5215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.5876 2.1073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.5648 3.5065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.7968 -1.2481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.6786 -0.7913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 7.5218 -1.3355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.7252 0.2017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.0970 -2.2659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.2220 -2.8307 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 3 2 1 1 1: 3 4 1 0 1: 4 5 2 0 1: 4 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 2 0 1: 8 10 1 0 1: 10 11 1 0 1: 11 12 1 0 1: 12 13 2 0 1: 12 14 1 0 1: 14 15 1 0 1: 15 16 1 0 1: 16 17 2 0 1: 16 18 1 0 1: 18 19 1 0 1: 19 20 1 0 1: 20 21 2 0 1: 20 22 1 0 1: 22 23 1 0 1: 23 24 1 0 1: 24 25 2 0 1: 24 26 1 0 1: 26 27 1 0 1: 27 28 1 0 1: 28 29 2 0 1: 28 30 1 0 1: 30 31 1 0 1: 31 32 1 0 1: 32 33 2 0 1: 32 34 1 0 1: 34 35 1 0 1: 35 36 1 0 1: 36 37 2 0 1: 36 38 1 0 1: 38 39 1 0 1: 39 40 1 0 1: 40 41 2 0 1: 40 42 1 0 1: 43 42 1 6 1: 43 44 1 0 1: 44 45 2 0 1: 44 46 1 0 1: 43 47 1 0 1: 47 48 1 0 1: 48 49 1 6 1: 48 50 1 0 1: 50 51 1 0 1: 51 52 2 0 1: 52 53 1 0 1: 47 54 1 1 1: 42 55 1 0 1: 39 56 1 6 1: 56 57 1 0 1: 56 58 1 0 1: 38 59 1 0 1: 35 60 1 6 1: 60 61 1 0 1: 61 62 1 0 1: 61 63 1 0 1: 34 64 1 0 1: 31 65 1 6 1: 65 66 1 0 1: 66 67 1 0 1: 66 68 1 0 1: 30 69 1 0 1: 27 70 1 6 1: 23 71 1 6 1: 19 72 1 6 1: 72 73 1 0 1: 73 74 1 0 1: 73 75 1 0 1: 18 76 1 0 1: 15 77 1 6 1: 77 78 1 0 1: 77 79 1 0 1: 11 80 1 6 1: 80 81 1 0 1: 81 82 1 0 1: 81 83 1 0 1: 10 84 1 0 1: 6 85 1 0 1: 46 3 1 0 1: M END 1: 1: single-double 1: RDKit 2D 1: 1: 17 16 0 0 0 0 0 0 0 0999 V2000 1: -6.9282 -0.2298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -6.0618 0.2696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.1962 -0.2312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.3298 0.2682 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.4642 -0.2326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.5978 0.2668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.7322 -0.2340 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8658 0.2654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0002 -0.2352 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8662 0.2640 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.7318 -0.2366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5982 0.2626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.4638 -0.2380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.3302 0.2612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.1958 -0.2394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.0622 0.2598 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.9278 -0.2408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 2 3 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 2 3 1: 11 12 1 0 1: 12 13 2 3 1: 13 14 1 0 1: 14 15 2 3 1: 15 16 1 0 1: 16 17 1 0 1: M END 1: 1: cis-trans 1: RDKit 2D 1: 1: 10 9 0 0 0 0 0 0 0 0999 V2000 1: -3.6370 -0.2028 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.7706 -0.7022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9050 -0.2016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.0386 -0.7008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1730 -0.2002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6934 -0.6994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5590 -0.1988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5582 0.8012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.4238 1.3020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.2902 0.8026 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 2 0 1: 3 4 1 0 1: 4 5 2 0 1: 5 6 1 0 1: 6 7 2 0 1: 7 8 1 0 1: 8 9 2 0 1: 9 10 1 0 1: M END 1: 1: admntn 1: RDKit 2D 1: 1: 10 12 0 0 0 0 0 0 0 0999 V2000 1: 1.3505 -0.5360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5267 -1.1020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4629 -1.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.7523 0.0052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4741 0.5660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4761 0.5032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3505 1.0730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.0611 0.5080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0643 0.5686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1877 -0.5490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 6 10 1 0 1: 8 1 1 0 1: 9 4 1 0 1: 10 2 1 0 1: M END 1: 39: [15:23:04] done 36: path: 2 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: 37: -------------------------- 37: -------------------------- 37: C/C=C/C(C)Cl 36: [15:23:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored 36: [15:23:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored 36: [15:23:04] Explicit valence for atom # 0 B, 5, is greater than permitted 36: [15:23:04] Explicit valence for atom # 1 C, 5, is greater than permitted 28/235 Test #39: graphmoltestPicklerGlobalSetting ....... Passed 0.08 sec test 40 Start 40: graphmolIterTest 40: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolIterTest 40: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 40: Test timeout computed to be: 1500 36: [15:23:04] Explicit valence for atom # 1 C, 5, is greater than permitted 36: [15:23:04] Explicit valence for atom # 1 C, 5, is greater than permitted 36: [15:23:04] Explicit valence for atom # 1 Si, 7, is greater than permitted 2: .... 2: ---------------------------------------------------------------------- 2: Ran 4 tests in 0.068s 2: 2: OK 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing reading existing pickle file (v2). 37: [15:23:04] Conflicting single bond directions around double bond at index 2. 37: [15:23:04] BondStereo set to STEREONONE and single bond directions set to NONE. 37: [15:23:04] Conflicting single bond directions around double bond at index 4. 37: [15:23:04] BondStereo set to STEREONONE and single bond directions set to NONE. 37: [15:23:04] Conflicting single bond directions around double bond at index 15. 37: [15:23:04] BondStereo set to STEREONONE and single bond directions set to NONE. 37: [15:23:04] Conflicting single bond directions around double bond at index 2. 37: [15:23:04] BondStereo set to STEREONONE and single bond directions set to NONE. 37: [15:23:04] Conflicting single bond directions around double bond at index 1. 37: [15:23:04] BondStereo set to STEREONONE and single bond directions set to NONE. 29/235 Test #40: graphmolIterTest ....................... Passed 0.09 sec 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing combining molecules using pickles. 38: Atoms: 38: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 38: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 38: 2 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 38: 3 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 38: 4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 38: 5 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: SP3 38: 6 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 38: Bonds: 38: 0 0->1 order: 1 38: 1 1->2 order: 1 38: 2 2->0 order: 1 38: 3 3->4 order: 1 38: 4 4->5 order: 1 38: 5 5->6 order: 1 38: 6 6->3 order: 1 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing Issue164: Roundtrip Pickle Failure. test 41 Start 41: hanoiTest 41: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/hanoiTest 41: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 41: Test timeout computed to be: 1500 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing Issue219: Pickle Failure with Conformations. 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing Issue220: Pickle problems with bond stereochemistry. 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing query serialization. 37: -------------------------------------------------- 30/235 Test #37: graphmoltestChirality .................. Passed 0.24 sec test 42 Start 42: graphmolMemTest1 42: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMemTest1 42: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 42: Test timeout computed to be: 1500 32: ...... 32: ---------------------------------------------------------------------- 32: Ran 6 tests in 0.025s 32: 32: OK 38: [15:23:04] C=[$(C=O)] 38: [15:23:04] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing radical handling in pickles. 38: [15:23:04] done 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing sf.net issue 2788233. 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing sf.net issue 3202580. 38: mass! 13.0034 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing sf.net issue 3316407. 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing sf.net issue 3496759. 38: smi match: *C *C 38: smi match: **=* **=* 38: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O 38: smi match: *OS(=O)OC *OS(=O)OC 38: smi match: *S(=O)(=O)OC *S(=O)(=O)OC 38: smi match: O=COC=O O=COC=O 38: smi match: OO OO 38: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F 38: smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1 38: smi match: nnnOC=O nnnOC=O 38: smi match: *=C=N *=C=N 38: smi match: OS(=O)(=O)C(F)(F)F OS(=O)(=O)C(F)(F)F 38: smi match: SP(S)=S SP(S)=S 38: smi match: NP(N)(N)=O NP(N)(N)=O 38: smi match: cN=[N+]=[N-] cN=[N+]=[N-] 38: smi match: *CC=O *CC=O 38: smi match: NNC=O NNC=O 38: smi match: * * 38: smi match: C=P C=P 38: smi match: CC(=N)Cl CC(=N)Cl 38: smi match: N=O N=O 38: smi match: ** ** 38: smi match: N=C=N N=C=N 38: smi match: [C-]#[NH+] [C-]#[NH+] 38: smi match: O=CON(C=O)C=O O=CON(C=O)C=O 38: smi match: N#CC[OH] N#CC[OH] 38: smi match: N#CC=O N#CC=O 38: smi match: N#CS(=O)=O N#CS(=O)=O 38: smi match: CCOP(=O)(C#N)OCC CCOP(=O)(C#N)OCC 38: smi match: N#CN=N N#CN=N 38: smi match: N=NCC=O N=NCC=O 31/235 Test #1: testCoordGen ........................... Passed 2.34 sec test 43 Start 43: resMolSupplierTest 43: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/resMolSupplierTest 43: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 43: Test timeout computed to be: 1500 38: smi match: CCCCCCC CCCCCCC 38: smi match: OCCOCCO OCCOCCO 38: smi match: SS SS 38: smi match: [SH] [SH] 38: smi match: *1CC1 *1CC1 38: smi match: [OH]ccc([OH])c[OH] [OH]ccc([OH])c[OH] 38: smi match: [OH]cc([OH])c[OH] [OH]cc([OH])c[OH] 38: smi match: NC(=S)N=N NC(=S)N=N 38: smi match: N#CS N#CS 38: smi match: cC[N+] cC[N+] 38: smi match: C*C=S C*C=S 38: smi match: N[CH2]C#N N[CH2]C#N 38: smi match: O=C1CCO1 O=C1CCO1 38: smi match: O=P([OH])OP(=O)[OH] O=P([OH])OP(=O)[OH] 38: smi match: O=C1CCN1 O=C1CCN1 38: smi match: O=C1C~CC(=O)C~C1 O=C1C~CC(=O)C~C1 38: smi match: C=CC=CC=CC=C C=CC=CC=CC=C 38: smi match: C1CCC(OC2CCC3CCCCC3C2)OC1 C1CCC(OC2CCC3CCCCC3C2)OC1 38: smi match: O=C1NCC2CCCCC21 O=C1NCC2CCCCC21 38: smi match: O=C1CCCC(=O)N1 O=C1CCCC(=O)N1 38: smi match: C1CCC(C2CCCO2)OC1 C1CCC(C2CCCO2)OC1 38: smi match: [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 38: smi match: C1CC2CCC(O1)O2 C1CC2CCC(O1)O2 38: smi match: cN(=O)~O cN(=O)~O 38: smi match: *[CH2]N1C(=O)CCC1=O *[CH2]N1C(=O)CCC1=O 38: smi match: N~NC=O N~NC=O 38: smi match: *=N~C *=N~C 41: [15:23:04] Testing the hanoi sort 41: [15:23:04] populating vectors 38: smi match: CO*(=O)=O CO*(=O)=O 38: smi match: * * 38: smi match: * * 38: smi match: *C=C *C=C 38: smi match: N#CS N#CS 38: smi match: *C=S *C=S 38: smi match: *N *N 38: smi match: *C(=C)C=O *C(=C)C=O 38: smi match: *C#C *C#C 38: smi match: N#CCO N#CCO 38: smi match: O=N(=O)CCO O=N(=O)CCO 38: smi match: N=CS N=CS 38: smi match: O=CNC(O)C=O O=CNC(O)C=O 38: smi match: C=C(C=O)C=O C=C(C=O)C=O 38: smi match: N=CC=O N=CC=O 38: smi match: *C(C=O)C=O *C(C=O)C=O 38: smi match: *C(C=O)=C(*)C=O *C(C=O)=C(*)C=O 38: smi match: O=CC=CC=O O=CC=CC=O 38: smi match: O=CN(O)C=O O=CN(O)C=O 38: smi match: O=CN(S)C=O O=CN(S)C=O 38: smi match: O=CNC=O O=CNC=O 38: smi match: O=CNN=O O=CNN=O 38: smi match: O=CNNC=O O=CNNC=O 38: smi match: O=CNOC=O O=CNOC=O 38: smi match: O=CS O=CS 38: smi match: O=CSC=S O=CSC=S 38: smi match: S=CS S=CS 38: smi match: C=O C=O 38: smi match: *C=N *C=N 38: smi match: CCCCCCC CCCCCCC 38: smi match: CN=O CN=O 38: smi match: CS(=O)(=O)O CS(=O)(=O)O 38: smi match: O=C1CCO1 O=C1CCO1 38: smi match: C=C(S)[SH]=O C=C(S)[SH]=O 38: smi match: C=CCO C=CCO 38: smi match: C=CC=N C=CC=N 38: smi match: C=CC=O C=CC=O 38: smi match: C=CC(=O)C=C C=CC(=O)C=C 38: smi match: C=CC=S C=CC=S 38: smi match: C=CC(=S)S C=CC(=S)S 38: smi match: *C=C(*)C=C *C=C(*)C=C 38: smi match: C=CC=N C=CC=N 38: smi match: *N(*)C=C *N(*)C=C 38: smi match: C=CN(=O)=O C=CN(=O)=O 38: smi match: C=CN(O)=O C=CN(O)=O 38: smi match: C=CO C=CO 38: smi match: C=COC=O C=COC=O 38: smi match: C=CS C=CS 38: smi match: C=C[SH](=O)=O C=C[SH](=O)=O 38: smi match: C=NCO C=NCO 38: smi match: C=NC=O C=NC=O 38: smi match: C=NN C=NN 38: smi match: C=NN=C C=NN=C 38: smi match: C=NO C=NO 38: smi match: C=NOC=O C=NOC=O 38: smi match: C=N=O C=N=O 38: smi match: N#CS N#CS 38: smi match: *CN=O *CN=O 38: smi match: NCN NCN 38: smi match: ON=CCN=O ON=CCN=O 38: smi match: NC(S)=N[SH](=O)=O NC(S)=N[SH](=O)=O 38: smi match: N=C(N)S N=C(N)S 38: smi match: NC(=O)Oc1ccccc1 NC(=O)Oc1ccccc1 38: smi match: NC=S NC=S 38: smi match: NC(N)=S NC(N)=S 38: smi match: C=CN C=CN 38: smi match: NOC=O NOC=O 38: smi match: C1CN1 C1CN1 38: smi match: O=C1NNNN1 O=C1NNNN1 38: smi match: N=C(N)C(=N)N N=C(N)C(=N)N 38: smi match: N=C(N)O N=C(N)O 38: smi match: N=C(N)C(=N)S N=C(N)C(=N)S 38: smi match: *C=N *C=N 38: smi match: N=CC=O N=CC=O 38: smi match: N=CS N=CS 38: smi match: N=C=N N=C=N 38: smi match: N=C=O N=C=O 38: smi match: N=C=S N=C=S 38: smi match: NOC(=O)O NOC(=O)O 38: smi match: *C(O)=S *C(O)=S 38: smi match: C=CO C=CO 32/235 Test #42: graphmolMemTest1 ....................... Passed 0.04 sec test 44 Start 44: molBundleTest 44: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/molBundleTest 44: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 44: Test timeout computed to be: 1500 29: 29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... 38: smi match: ON=CC=NO ON=CC=NO 38: smi match: *C[SH](=O)=O *C[SH](=O)=O 38: smi match: OS(=O)=O OS(=O)=O 38: smi match: N#CS N#CS 38: smi match: C=C(S)S C=C(S)S 38: smi match: N=C(N)S N=C(N)S 38: smi match: N=C(S)S N=C(S)S 38: smi match: NC(=S)S NC(=S)S 38: smi match: O=CNS O=CNS 38: smi match: S S 38: smi match: [SiH4] [SiH4] 38: smi match: NS NS 38: smi match: NCN NCN 38: smi match: cC(c)(O)O cC(c)(O)O 38: smi match: *C(c)O *C(c)O 38: smi match: C=CS(c)(=O)=O C=CS(c)(=O)=O 38: smi match: cS(=O)(=O)O cS(=O)(=O)O 38: smi match: *c1ccccn1=O *c1ccccn1=O 38: smi match: *c1ccccn1 *c1ccccn1 38: smi match: *c1nccccn1 *c1nccccn1 38: smi match: C1COCOC1 C1COCOC1 38: smi match: C=S C=S 38: smi match: c=S c=S 38: smi match: S=CS S=CS 38: smi match: C=CN(=O)=O C=CN(=O)=O 38: smi match: C=CN(=O)O C=CN(=O)O 38: smi match: N=CC=O N=CC=O 38: smi match: C=CS C=CS 38: smi match: SC(S)(S)S SC(S)(S)S 38: smi match: OS(O)(O)O OS(O)(O)O 38: smi match: O=N(=O)C[SH](=O)=O O=N(=O)C[SH](=O)=O 38: smi match: O=N(O)C[SH](=O)=O O=N(O)C[SH](=O)=O 38: smi match: N#CS N#CS 38: smi match: C=NO C=NO 38: smi match: C=N[SH]=N C=N[SH]=N 38: smi match: O=C(S)S O=C(S)S 38: smi match: N=C(S)S N=C(S)S 38: smi match: N=C(=N)S N=C(=N)S 38: smi match: O=N=O O=N=O 38: smi match: O=NO O=NO 38: smi match: ONO ONO 38: smi match: C1SCS1 C1SCS1 38: smi match: N=C=S N=C=S 38: smi match: N=C=N N=C=N 38: smi match: C1N=N1 C1N=N1 38: smi match: *CS *CS 38: smi match: SC(S)=C(S)S SC(S)=C(S)S 38: smi match: N=CC=NO N=CC=NO 38: smi match: N#CCC#N N#CCC#N 38: smi match: CON=O CON=O 38: smi match: C=CN C=CN 38: smi match: C=N[SH](=O)=O C=N[SH](=O)=O 38: smi match: NN=O NN=O 38: smi match: NC(=O)S NC(=O)S 38: smi match: N#CS N#CS 38: smi match: NC(=O)C(N)=O NC(=O)C(N)=O 38: smi match: c=N c=N 38: smi match: C1COCO1 C1COCO1 38: smi match: C=NN[SH](=O)=O C=NN[SH](=O)=O 38: smi match: O=CC=O O=CC=O 38: smi match: O=CNOC=O O=CNOC=O 38: smi match: O=C1C=CC(=O)C=C1 O=C1C=CC(=O)C=C1 38: smi match: ONO ONO 38: smi match: ON(~O)~O ON(~O)~O 38: smi match: OC1COC(O)C1 OC1COC(O)C1 38: smi match: OC1CCOC1O OC1CCOC1O 38: smi match: OC1CCOC(O)C1 OC1CCOC(O)C1 38: smi match: N=[N+]=N N=[N+]=N 38: smi match: N#CN N#CN 38: smi match: C=NN=C C=NN=C 38: smi match: *CCN(C)C *CCN(C)C 38: smi match: CNN CNN 38: smi match: *CC *CC 38: smi match: OCS OCS 38: smi match: C1NO1 C1NO1 38: smi match: COS(C)(=O)=O COS(C)(=O)=O 38: smi match: C1CO1 C1CO1 38: smi match: *c1-c-c-ccN1 *c1-c-c-ccN1 38: smi match: *C(*)=C *C(*)=C 38: smi match: N#[NH+] N#[NH+] 38: smi match: C#NO C#NO 38: smi match: OOO OOO 38: smi match: OO OO 38: smi match: O~Cl(~O)~O O~Cl(~O)~O 38: smi match: O~Cl(~O)(~O)~O O~Cl(~O)(~O)~O 38: smi match: [OH]~C(~O)~O [OH]~C(~O)~O 38: smi match: *N *N 38: smi match: *P *P 38: smi match: *S *S 38: smi match: *C(*)(*)C=C *C(*)(*)C=C 38: smi match: *C(*)(*)C=C *C(*)(*)C=C 38: smi match: *C(*)C=C *C(*)C=C 38: smi match: *CC=C *CC=C 38: smi match: CN=C=O CN=C=O 38: smi match: CN=C=S CN=C=S 38: smi match: *C=O *C=O 38: smi match: N=N N=N 38: smi match: SS SS 38: smi match: O=C1CCNC(=O)O1 O=C1CCNC(=O)O1 38: smi match: CSC(C)=N CSC(C)=N 38: smi match: COC(C)=N COC(C)=N 38: smi match: C=C=C C=C=C 38: smi match: *C(=O)OC=O *C(=O)OC=O 38: smi match: C=CC#N C=CC#N 38: smi match: C=CC=O C=CC=O 38: smi match: CC=CC(C)=O CC=CC(C)=O 38: smi match: CC=CC(=O)OCC CC=CC(=O)OCC 38: smi match: C#CC#N C#CC#N 38: smi match: C#CC=O C#CC=O 38: smi match: C#CC(=O)OCC C#CC(=O)OCC 38: smi match: C#CC=O C#CC=O 38: smi match: *C(=O)C#C *C(=O)C#C 38: smi match: C=CC=O C=CC=O 38: smi match: *C(*)(*)O *C(*)(*)O 38: smi match: COS(O)(=O)=O COS(O)(=O)=O 38: smi match: CS(=O)(=O)[O-] CS(=O)(=O)[O-] 38: smi match: NS(=O)(=O)[O-] NS(=O)(=O)[O-] 38: smi match: *C(*)(*)C=O *C(*)(*)C=O 38: smi match: *C(*)(*)C=O *C(*)(*)C=O 38: smi match: *C(*)C=O *C(*)C=O 38: smi match: *CC=O *CC=O 38: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 38: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 38: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O 38: smi match: *C[SH](=O)=O *C[SH](=O)=O 38: smi match: * * 38: smi match: *1CC1 *1CC1 38: smi match: O=COC=O O=COC=O 38: smi match: N=C=O N=C=O 38: smi match: N=C=S N=C=S 38: smi match: O~O O~O 38: smi match: N~[SiH4] N~[SiH4] 38: smi match: *P *P 38: smi match: C=N=N C=N=N 38: smi match: *N#[NH+] *N#[NH+] 38: smi match: *S* *S* 38: smi match: ** ** 38: smi match: *CC* *CC* 38: smi match: *O[SiH3] *O[SiH3] 38: smi match: *OS(*)~O *OS(*)~O 38: smi match: N~N~O N~N~O 38: smi match: *N(~O)(~O)~O *N(~O)(~O)~O 38: smi match: *[N+](=C)[O-] *[N+](=C)[O-] 38: smi match: * * 38: smi match: *C(*)NCN(*)* *C(*)NCN(*)* 38: smi match: *OCC#N *OCC#N 38: smi match: **C=C **C=C 38: smi match: C=C[O-] C=C[O-] 38: smi match: C=CO C=CO 38: smi match: * * 38: smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O 38: smi match: O=COn1ccnc1 O=COn1ccnc1 38: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F 38: smi match: CC(C)(C)S CC(C)(C)S 38: 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 38: smi match: [CH]=O [CH]=O 38: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C 38: smi match: SS SS 38: smi match: [SH] [SH] 38: smi match: *C* *C* 38: smi match: * * 38: smi match: C[nH3+] C[nH3+] 38: smi match: cC(=N)[NH2] cC(=N)[NH2] 38: smi match: O=CN[OH] O=CN[OH] 38: smi match: NN NN 38: smi match: * * 38: smi match: *OP(=O)O* *OP(=O)O* 38: smi match: * * 38: smi match: * * 38: smi match: * * 33/235 Test #44: molBundleTest .......................... Passed 0.06 sec test 45 Start 45: testSGroup 45: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/testSGroup 45: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 45: Test timeout computed to be: 1500 38: smi match: *N=C(*)* *N=C(*)* 38: smi match: *C(*)(*)C=O *C(*)(*)C=O 38: smi match: CSC=O CSC=O 38: smi match: * * 38: smi match: O=CCl O=CCl 38: smi match: *** *** 38: smi match: *C=O *C=O 38: smi match: C[OH] C[OH] 38: smi match: C[OH] C[OH] 38: smi match: C[OH] C[OH] 38: smi match: C[OH] C[OH] 38: smi match: C[CH]=O C[CH]=O 38: smi match: *=* *=* 38: smi match: *C *C 38: smi match: C#C C#C 38: smi match: *[CH]C=C *[CH]C=C 38: smi match: cCC(=O)[OH] cCC(=O)[OH] 38: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] 38: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] 38: smi match: C=CC(=O)[OH] C=CC(=O)[OH] 38: smi match: N#CC(=O)[OH] N#CC(=O)[OH] 38: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O 38: smi match: *N(*)C*=O *N(*)C*=O 38: smi match: O=*C[OH] O=*C[OH] 38: smi match: *=C*=O *=C*=O 38: smi match: *=CC#N *=CC#N 38: smi match: *C[OH] *C[OH] 38: smi match: ** ** 38: smi match: *C[OH] *C[OH] 38: smi match: *C(*)=O *C(*)=O 38: smi match: * * 38: smi match: *CC(=O)[OH] *CC(=O)[OH] 38: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O 38: smi match: *c *c 38: smi match: CN(C)c CN(C)c 38: smi match: c c 38: smi match: *c *c 38: smi match: *c *c 38: smi match: **:*cF **:*cF 38: smi match: cB([OH])[OH] cB([OH])[OH] 38: smi match: N~N~N N~N~N 38: smi match: *N=N* *N=N* 38: smi match: *CC[OH] *CC[OH] 36: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 38: smi match: *CC[OH] *CC[OH] 38: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] 38: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] 38: smi match: *CCC(=O)[OH] *CCC(=O)[OH] 38: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] 38: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O 38: smi match: *OC(*)=O *OC(*)=O 38: smi match: *C(=O)[OH] *C(=O)[OH] 38: smi match: O=C[OH] O=C[OH] 38: smi match: *OC(=O)O* *OC(=O)O* 38: smi match: * * 38: smi match: *OC(=O)Cl *OC(=O)Cl 38: smi match: *C#N *C#N 38: smi match: NCC(=O)NCC=O NCC(=O)NCC=O 38: smi match: SS SS 38: smi match: * * 38: smi match: *=* *=* 38: smi match: *=* *=* 38: smi match: *=* *=* 38: smi match: *=* *=* 38: smi match: C1CO1 C1CO1 38: smi match: *OC(*)=O *OC(*)=O 38: smi match: * * 38: smi match: *O*[OH] *O*[OH] 38: smi match: COC(C)(C)O COC(C)(C)O 38: smi match: *[OH] *[OH] 38: smi match: ** ** 38: smi match: C=N[NH2] C=N[NH2] 38: smi match: C=NC=O C=NC=O 38: smi match: * * 38: smi match: C#NC C#NC 38: smi match: CN=C=O CN=C=O 38: smi match: CN=C=S CN=C=S 38: smi match: *OC(*)(*)O* *OC(*)(*)O* 38: smi match: *C(*)=O *C(*)=O 38: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C 38: smi match: *~*=O *~*=O 38: smi match: *~*=O *~*=O 38: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] 38: smi match: * * 38: smi match: *C#N *C#N 38: smi match: *N(=O)~O *N(=O)~O 38: smi match: N N 38: smi match: OC(=O)C(O)=O OC(=O)C(O)=O 38: smi match: C=NO C=NO 38: smi match: O~O O~O 38: smi match: c[OH] c[OH] 38: smi match: O=P(~[OH])~O O=P(~[OH])~O 38: smi match: CO~P(=O)~O CO~P(=O)~O 38: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O 38: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O 38: smi match: O=P(~O)~O O=P(~O)~O 38: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O 38: smi match: C[NH2] C[NH2] 38: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 38: smi match: * * 38: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 38: smi match: CS(C)~O CS(C)~O 38: smi match: CS(C)(~O)~O CS(C)(~O)~O 38: smi match: CS(N)(~O)~O CS(N)(~O)~O 38: smi match: CS([OH])(~O)~O CS([OH])(~O)~O 38: smi match: COS(C)(~O)~O COS(C)(~O)~O 38: smi match: *S(C)(~O)~O *S(C)(~O)~O 38: smi match: CN(C)C CN(C)C 38: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 38: smi match: *C(*)=S *C(*)=S 38: smi match: *OC(*)=S *OC(*)=S 38: smi match: * * 38: smi match: C[SH] C[SH] 38: smi match: c[SH] c[SH] 38: smi match: NC(N)=S NC(N)=S 38: smi match: * * 38: smi match: ***** ***** 38: smi match: NC(N)=O NC(N)=O 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing sf.net issue 280. 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing sf.net issue 285. 38: [15:23:04] done 38: [15:23:04] done 38: [15:23:04] done 38: [15:23:04] done 38: [15:23:04] done 38: [15:23:04] done 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing Github2441: Add RDProps interface to Conformers. 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing Issue2510: Pickle Confs as double. 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing Github #2465: Negative atom-map numbers cause depickling to fail. 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing loading pickled mols with conformers 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing conformer reading/writing options 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing property reading options 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing property reading options 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing boost::serialization integration 34/235 Test #32: pyDistGeom ............................. Passed 0.53 sec test 46 Start 46: test-valgrind 46: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/test-valgrind 46: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 46: Test timeout computed to be: 1500 38: [15:23:04] done 38: [15:23:04] ------------------------------------- 38: [15:23:04] Testing github issue 6036 35/235 Test #38: graphmoltestPickler .................... Passed 0.38 sec test 47 Start 47: graphmolTestsCatch 47: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 47: Test timeout computed to be: 1500 36: [15:23:04] non-ring atom 0 marked aromatic 36: [15:23:04] non-ring atom 0 marked aromatic 36: [15:23:04] Conflicting single bond directions around double bond at index 17. 36: [15:23:04] BondStereo set to STEREONONE and single bond directions set to NONE. 36/235 Test #2: pyCoordGen ............................. Passed 2.49 sec 36: starting ring finding test 48 Start 48: graphmolOrganometallicsCatch 48: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch 48: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 48: Test timeout computed to be: 1500 36: done 36: starting ring finding 36: done 36: starting ring finding 36: done 36: 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 36: starting sanitization 37/235 Test #46: test-valgrind .......................... Passed 0.06 sec test 49 Start 49: graphmolSGroupCatch 49: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolSGroupCatch 49: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 49: Test timeout computed to be: 1500 36: done 36: starting sanitization 36: done 47: Randomness seeded to: 1355612572 47: [15:23:05] WARNING: not removing hydrogen atom without neighbors 47: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 47: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 47: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 47: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 47: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 47: [15:23:05] Explicit valence for atom # 1 N, 5, is greater than permitted 47: [15:23:05] Explicit valence for atom # 1 N, 6, is greater than permitted 47: [15:23:05] Explicit valence for atom # 1 N, 5, is greater than permitted 47: [15:23:05] Explicit valence for atom # 1 N, 5, is greater than permitted 47: [15:23:05] Explicit valence for atom # 2 O, 3, is greater than permitted 47: [15:23:05] Explicit valence for atom # 2 O, 3, is greater than permitted 47: [15:23:05] non-ring atom 2 marked aromatic 47: [15:23:05] non-ring atom 2 marked aromatic 47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 1 2 3 47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 1 2 3 47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 47: [15:23:05] Explicit valence for atom # 1 O, 3, is greater than permitted 47: [15:23:05] Explicit valence for atom # 4 F, 2, is greater than permitted 47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 6 7 8 47: [15:23:05] Explicit valence for atom # 1 C, 5, is greater than permitted 47: [15:23:05] WARNING: not removing hydrogen atom with dummy atom neighbors 47: [15:23:05] WARNING: not removing hydrogen atom with dummy atom neighbors 47: [15:23:05] WARNING: not removing hydrogen atom with wedged bond 47: [15:23:05] WARNING: not removing hydrogen atom without neighbors 47: [15:23:05] WARNING: not removing hydrogen atom without neighbors 38/235 Test #45: testSGroup ............................. Passed 0.14 sec test 50 Start 50: graphmolAdjustQueryCatch 50: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch 50: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 50: Test timeout computed to be: 1500 47: [15:23:05] WARNING: not removing hydrogen atom without neighbors 47: [15:23:05] WARNING: not removing hydrogen atom without neighbors 47: [15:23:05] Unreasonable formal charge on atom # 0. 36: starting ring finding 36: done 36: starting ring finding 36: done 36: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 47: [15:23:05] 47: 47: **** 47: Pre-condition Violation 47: no atom 47: Violation occurred on line 181 in file ./Code/GraphMol/ROMol.cpp 47: Failed Expression: at 47: ---------- 47: Stacktrace: 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 47: 3# 0x0000AAAAE40BAC84 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: 36: [15:23:05] WARNING: not removing hydrogen atom with dummy atom neighbors 30: ...[15:23:05] Molecule does not have explicit Hs. Consider calling AddHs() 47: [15:23:05] 47: 47: **** 47: Pre-condition Violation 47: no owner 47: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 47: Failed Expression: dp_mol 47: ---------- 47: Stacktrace: 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 47: 3# 0x0000AAAAE40BACF8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: 47: [15:23:05] 47: 47: **** 47: Pre-condition Violation 47: atom not associated with this molecule 47: Violation occurred on line 182 in file ./Code/GraphMol/ROMol.cpp 47: Failed Expression: &at->getOwningMol() == this 47: ---------- 47: Stacktrace: 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 47: 3# 0x0000AAAAE40BAD78 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: 47: [15:23:05] 47: 47: **** 47: Pre-condition Violation 47: no atom 47: Violation occurred on line 364 in file ./Code/GraphMol/ROMol.cpp 47: Failed Expression: at 47: ---------- 47: Stacktrace: 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 47: 3# 0x0000AAAAE40BAE40 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: 47: [15:23:05] 47: 47: **** 47: Pre-condition Violation 47: no owner 47: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 47: Failed Expression: dp_mol 47: ---------- 47: Stacktrace: 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 47: 3# 0x0000AAAAE40BAEB8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: 47: [15:23:05] 47: 47: **** 47: Pre-condition Violation 47: atom not associated with this molecule 47: Violation occurred on line 365 in file ./Code/GraphMol/ROMol.cpp 47: Failed Expression: &at->getOwningMol() == this 47: ---------- 47: Stacktrace: 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 47: 3# 0x0000AAAAE40BAF3C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: 47: [15:23:05] 47: 47: **** 47: Pre-condition Violation 47: no atom 47: Violation occurred on line 371 in file ./Code/GraphMol/ROMol.cpp 47: Failed Expression: at 47: ---------- 47: Stacktrace: 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 47: 3# 0x0000AAAAE40BB650 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: 47: [15:23:05] 47: 47: **** 47: Pre-condition Violation 47: no owner 47: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 47: Failed Expression: dp_mol 47: ---------- 47: Stacktrace: 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 47: 3# 0x0000AAAAE40BB06C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: 47: [15:23:05] 47: 47: **** 47: Pre-condition Violation 47: atom not associated with this molecule 47: Violation occurred on line 372 in file ./Code/GraphMol/ROMol.cpp 47: Failed Expression: &at->getOwningMol() == this 47: ---------- 47: Stacktrace: 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 47: 3# 0x0000AAAAE40BB0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: 47: [15:23:05] 47: 47: **** 47: Pre-condition Violation 47: null atom passed in 47: Violation occurred on line 386 in file ./Code/GraphMol/ROMol.cpp 47: Failed Expression: atom_pin 47: ---------- 47: Stacktrace: 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 47: 3# 0x0000AAAAE40BB634 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: 47: [15:23:05] 47: 47: **** 47: Pre-condition Violation 47: cannot take ownership of an atom which already has an owner 47: Violation occurred on line 387 in file ./Code/GraphMol/ROMol.cpp 47: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this 47: ---------- 47: Stacktrace: 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 47: 3# 0x0000AAAAE40BB2E0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: 47: [15:23:05] 47: 47: **** 47: Pre-condition Violation 47: cannot take ownership of an bond which already has an owner 47: Violation occurred on line 412 in file ./Code/GraphMol/ROMol.cpp 47: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this 47: ---------- 47: Stacktrace: 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 47: 3# 0x0000AAAAE40BB614 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: 47: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 47: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 47: [15:23:05] WARNING: not removing hydrogen atom without neighbors 47: [15:23:05] Explicit valence for atom # 1 F greater than permitted 47: [15:23:05] 47: 47: **** 47: Pre-condition Violation 47: plain atoms have no Query 47: Violation occurred on line 691 in file ./Code/GraphMol/Atom.cpp 47: Failed Expression: 0 47: ---------- 47: Stacktrace: 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::Atom::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 47: 3# 0x0000AAAAE406B0EC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: 47: [15:23:05] 47: 47: **** 47: Pre-condition Violation 47: plain atoms have no Query 47: Violation occurred on line 696 in file ./Code/GraphMol/Atom.cpp 47: Failed Expression: 0 47: ---------- 47: Stacktrace: 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::Atom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 47: 3# 0x0000AAAAE406B178 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: 47: [15:23:05] 47: 47: **** 47: Pre-condition Violation 47: plain bonds have no Query 47: Violation occurred on line 207 in file ./Code/GraphMol/Bond.cpp 47: Failed Expression: 0 47: ---------- 47: Stacktrace: 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::Bond::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 47: 3# 0x0000AAAAE406AD3C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: 47: [15:23:05] 47: 47: **** 47: Pre-condition Violation 47: plain bonds have no query 47: Violation occurred on line 228 in file ./Code/GraphMol/Bond.cpp 47: Failed Expression: 0 47: ---------- 47: Stacktrace: 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::Bond::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 47: 3# 0x0000AAAAE406ADC8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: 47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 36: ------------------------------- 36: [15:23:05] Explicit valence for atom # 0 N, 4, is greater than permitted 48: Randomness seeded to: 1685663689 48: =============================================================================== 48: All tests passed (62 assertions in 6 test cases) 48: 39/235 Test #48: graphmolOrganometallicsCatch ........... Passed 0.07 sec test 51 Start 51: chiralityTestsCatch 51: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/chiralityTestsCatch 51: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 51: Test timeout computed to be: 1500 36: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 36: [15:23:05] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 36: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 36: [15:23:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 36: [15:23:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 36: [15:23:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 36: [15:23:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 36: [15:23:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 36: 47: [15:23:05] Unusual charge on atom 0 number of radical electrons set to zero 47: [15:23:05] Unusual charge on atom 0 number of radical electrons set to zero 47: [15:23:05] Unusual charge on atom 0 number of radical electrons set to zero 47: [15:23:05] non-ring atom 0 marked aromatic 47: [15:23:05] non-ring atom 0 marked aromatic 47: [15:23:05] Explicit valence for atom # 1 C, 5, is greater than permitted 47: [15:23:05] Explicit valence for atom # 9 C, 5, is greater than permitted 47: [15:23:05] Explicit valence for atom # 3 N, 4, is greater than permitted 47: [15:23:05] Explicit valence for atom # 15 C, 5, is greater than permitted 47: [15:23:05] Explicit valence for atom # 11 C, 5, is greater than permitted 47: [15:23:05] Explicit valence for atom # 9 C, 5, is greater than permitted 47: [15:23:05] Explicit valence for atom # 9 C, 5, is greater than permitted 47: [15:23:05] Explicit valence for atom # 9 C, 6, is greater than permitted 47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 7 47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 3 47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 3 7 47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 3 7 47: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 47: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 36: [15:23:05] WARNING: not removing hydrogen atom with dummy atom neighbors 49: Randomness seeded to: 2437238120 49: =============================================================================== 49: All tests passed (136 assertions in 8 test cases) 49: 40/235 Test #49: graphmolSGroupCatch .................... Passed 0.10 sec test 52 Start 52: canonTestsCatch 52: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/canonTestsCatch 52: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 52: Test timeout computed to be: 1500 47: [15:23:05] Explicit valence for atom # 1 O, 3, is greater than permitted 47: [15:23:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 47: [15:23:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 47: [15:23:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 47: [15:23:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 47: [15:23:05] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. 47: [15:23:05] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom 47: [15:23:05] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom 41: [15:23:05] sorting (hanoi sort) vectors 51: Randomness seeded to: 2409308902 50: Randomness seeded to: 1434556895 50: =============================================================================== 50: All tests passed (283 assertions in 11 test cases) 50: 41/235 Test #50: graphmolAdjustQueryCatch ............... Passed 0.14 sec test 53 Start 53: moliteratorTestsCatch 53: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/moliteratorTestsCatch 53: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 53: Test timeout computed to be: 1500 51: [15:23:05] unable to set wavy bonds for double bonds: 3 47: [15:23:05] non-ring atom 0 marked aromatic 47: [15:23:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 47: [15:23:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 51: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 51: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 47: [15:23:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 47: [15:23:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 51: [15:23:05] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. 51: [15:23:05] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. 51: [15:23:05] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored 47: [15:23:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 47: [15:23:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 47: [15:23:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 47: [15:23:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 47: [15:23:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 47: [15:23:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 51: =============================================================================== 51: All tests passed (2267 assertions in 79 test cases) 51: 42/235 Test #51: chiralityTestsCatch .................... Passed 0.23 sec test 54 Start 54: queryTestsCatch 54: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/queryTestsCatch 54: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 54: Test timeout computed to be: 1500 47: [15:23:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 47: [15:23:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 47: [15:23:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 30: ......[15:23:05] Molecule does not have explicit Hs. Consider calling AddHs() 36: [15:23:05] Maximum BFS search size exceeded. 36: This is likely due to a highly symmetric fused ring system. 53: Randomness seeded to: 317281418 53: =============================================================================== 53: All tests passed (14 assertions in 4 test cases) 53: 43/235 Test #53: moliteratorTestsCatch .................. Passed 0.27 sec test 55 Start 55: molbundleTestsCatch 55: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/molbundleTestsCatch 55: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 55: Test timeout computed to be: 1500 47: [15:23:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 47: [15:23:05] Explicit valence for atom # 0 Al, 6, is greater than permitted 47: [15:23:05] Explicit valence for atom # 0 Al, 6, is greater than permitted 47: [15:23:05] Explicit valence for atom # 1 Si, 6, is greater than permitted 47: [15:23:05] Explicit valence for atom # 1 Si, 6, is greater than permitted 47: [15:23:05] Explicit valence for atom # 0 P, 6, is greater than permitted 47: [15:23:05] Explicit valence for atom # 0 P, 6, is greater than permitted 47: [15:23:05] Explicit valence for atom # 0 P, 7, is greater than permitted 47: [15:23:05] Explicit valence for atom # 0 P, 7, is greater than permitted 47: [15:23:05] Explicit valence for atom # 1 As, 6, is greater than permitted 47: [15:23:05] Explicit valence for atom # 1 As, 6, is greater than permitted 47: [15:23:05] Explicit valence for atom # 1 As, 7, is greater than permitted 47: [15:23:05] Explicit valence for atom # 1 As, 7, is greater than permitted 47: [15:23:05] Explicit valence for atom # 0 Sb, 6, is greater than permitted 47: [15:23:05] Explicit valence for atom # 0 Sb, 6, is greater than permitted 47: [15:23:05] Explicit valence for atom # 0 Sb, 7, is greater than permitted 47: [15:23:05] Explicit valence for atom # 0 Sb, 7, is greater than permitted 47: [15:23:05] Explicit valence for atom # 1 Bi, 6, is greater than permitted 47: [15:23:05] Explicit valence for atom # 1 Bi, 6, is greater than permitted 47: [15:23:05] Explicit valence for atom # 1 Bi, 8, is greater than permitted 47: [15:23:05] Explicit valence for atom # 1 Bi, 8, is greater than permitted 47: =============================================================================== 47: All tests passed (4464 assertions in 106 test cases) 47: 44/235 Test #47: graphmolTestsCatch ..................... Passed 0.50 sec test 56 Start 56: pickleTestsCatch 56: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/pickleTestsCatch 56: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 56: Test timeout computed to be: 1500 30: ... 30: ---------------------------------------------------------------------- 30: Ran 12 tests in 0.729s 30: 30: OK 56: Randomness seeded to: 4178049553 56: =============================================================================== 56: All tests passed (45 assertions in 4 test cases) 56: 45/235 Test #56: pickleTestsCatch ....................... Passed 0.11 sec test 57 Start 57: tableTestsCatch 57: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/tableTestsCatch 57: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 57: Test timeout computed to be: 1500 54: Randomness seeded to: 217692736 54: =============================================================================== 54: All tests passed (10 assertions in 1 test case) 54: 46/235 Test #54: queryTestsCatch ........................ Passed 0.36 sec test 58 Start 58: molopsTestsCatch 58: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/molopsTestsCatch 58: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 58: Test timeout computed to be: 1500 58: Randomness seeded to: 1260422142 58: =============================================================================== 58: All tests passed (79 assertions in 6 test cases) 58: 47/235 Test #58: molopsTestsCatch ....................... Passed 0.05 sec test 59 Start 59: smiTest1 59: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 59: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 59: Test timeout computed to be: 1500 36: [15:23:05] Maximum BFS search size exceeded. 36: This is likely due to a highly symmetric fused ring system. 48/235 Test #30: pyForceFieldConstraints ................ Passed 1.44 sec test 60 Start 60: smiTest2 60: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 60: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 60: Test timeout computed to be: 1500 36: F/C=C/Cl 36: [H]/C(F)=C(/[H])Cl 36: F/C=C/Cl 36: F/C=C/Cl 36: C/C(F)=C(/C)Cl 36: [15:23:05] ----------------------- 36: Testing isRingFused 59: [15:23:05] WARNING: not removing hydrogen atom without neighbors 59: [15:23:05] WARNING: not removing hydrogen atom without neighbors 59: [15:23:05] WARNING: not removing hydrogen atom without neighbors 59: [15:23:05] WARNING: not removing hydrogen atom without neighbors 59: [15:23:05] WARNING: not removing hydrogen atom without neighbors 59: [15:23:05] WARNING: not removing hydrogen atom without neighbors 59: [15:23:05] WARNING: not removing hydrogen atom without neighbors 59: [15:23:05] WARNING: not removing hydrogen atom without neighbors 59: [15:23:05] WARNING: not removing hydrogen atom without neighbors 59: [15:23:05] WARNING: not removing hydrogen atom without neighbors 49/235 Test #36: graphmolMolOpsTest ..................... Passed 1.30 sec test 61 Start 61: cxsmilesTest 61: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest 61: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 61: Test timeout computed to be: 1500 60: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' 60: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' 60: [15:23:05] SMILES Parse Error: syntax error while parsing: - 60: [15:23:05] SMILES Parse Error: check for mistakes around position 1: 60: [15:23:05] - 60: [15:23:05] ^ 60: [15:23:05] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' 60: [15:23:05] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' 60: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' 60: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' 60: [15:23:05] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' 60: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' 60: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' 60: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' 60: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' 60: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' 60: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' 60: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' 59: [15:23:05] WARNING: not removing hydrogen atom without neighbors 59: [15:23:05] Invalid chiral specification on atom 0 59: [15:23:05] Invalid chiral specification on atom 0 59: [15:23:05] Invalid chiral specification on atom 0 59: [15:23:05] Invalid chiral specification on atom 0 59: [15:23:05] Invalid chiral specification on atom 0 50/235 Test #60: smiTest2 ............................... Passed 0.03 sec test 62 Start 62: smaTest1 62: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 62: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 62: Test timeout computed to be: 1500 59: [15:23:05] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' 59: [15:23:05] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' 55: Randomness seeded to: 754812182 55: =============================================================================== 55: All tests passed (6 assertions in 1 test case) 55: 51/235 Test #55: molbundleTestsCatch .................... Passed 0.46 sec test 63 Start 63: smiTestCatch 63: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 63: Test timeout computed to be: 1500 57: Randomness seeded to: 3729418531 57: =============================================================================== 57: All tests passed (7 assertions in 2 test cases) 57: 62: [15:23:05] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC 62: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' 62: [15:23:05] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON 62: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' 63: Randomness seeded to: 3100898158 63: [15:23:05] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 63: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 63: [15:23:05] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' 52/235 Test #57: tableTestsCatch ........................ Passed 0.36 sec test 64 Start 64: nontetrahedralCatch 64: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch 64: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 64: Test timeout computed to be: 1500 63: [15:23:05] SMARTS Parse Error: unclosed ring for input: 'C1C' 63: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 62: [15:23:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 62: [15:23:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 63: [15:23:05] SMARTS Parse Error: syntax error while parsing: C)foo 63: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' 63: [15:23:05] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| 63: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' 63: [15:23:05] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' 59: --C1CCC2(CC1)CCCCC2CCC1CCCC1 53/235 Test #62: smaTest1 ............................... Passed 0.16 sec test 65 Start 65: v2smiTestCatch 65: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch 65: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 65: Test timeout computed to be: 1500 64: Randomness seeded to: 4082872462 64: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 64: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 64: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 64: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 64: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 64: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 59: smi: ClC1CCCCC1 59: smi: ClC1CCCCC1 59: smi: ClC1CCCCC1Br 59: smi: c1ccccc1 59: smi: c1ccncc1 59: smi: c1cc[nH]c1 59: smi: c1cc[nH]c1 59: smi: c1cc[pH]c1 59: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 59: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 59: CbC(aC)aC 59: CaC(bC)aC 59: CbC(bC)aC 59: O.C 59: 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 59: [15:23:05] SMILES Parse Error: syntax error while parsing: c%()ccccc%() 59: [15:23:05] SMILES Parse Error: check for mistakes around position 4: 59: [15:23:05] c%()ccccc%() 59: [15:23:05] ~~~^ 59: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' 59: [15:23:05] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) 59: [15:23:05] SMILES Parse Error: check for mistakes around position 9: 59: [15:23:05] c%(100000)ccccc%(100000) 59: [15:23:05] ~~~~~~~~^ 59: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' 59: [15:23:05] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' 59: [15:23:05] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' 59: [15:23:05] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# 59: [15:23:05] SMILES Parse Error: check for mistakes around position 14: 59: [15:23:05] COc(c1)cccc1C# 59: [15:23:05] ~~~~~~~~~~~~~^ 59: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 59: [15:23:05] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# 59: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 59: [15:23:05] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# 59: [15:23:05] SMILES Parse Error: check for mistakes around position 14: 59: [15:23:05] COc(c1)cccc1C# 59: [15:23:05] ~~~~~~~~~~~~~^ 59: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 59: [15:23:05] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# 59: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 59: [15:23:05] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# 59: [15:23:05] SMILES Parse Error: check for mistakes around position 14: 59: [15:23:05] COc(c1)cccc1C# 59: [15:23:05] ~~~~~~~~~~~~~^ 59: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 59: [15:23:05] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# 59: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 59: C=c1s/c2n(c1=O)CCCCCCC\N=2 59: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 59: [15:23:05] SMILES Parse Error: extra close parentheses while parsing: C) 59: [15:23:05] SMILES Parse Error: check for mistakes around position 2: 59: [15:23:05] C) 59: [15:23:05] ~^ 59: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' 64: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 64: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 54/235 Test #59: smiTest1 ............................... Passed 0.28 sec test 66 Start 66: testDepictor 66: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/testDepictor 66: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor 66: Test timeout computed to be: 1500 64: [15:23:06] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. 64: =============================================================================== 64: All tests passed (308 assertions in 9 test cases) 64: 55/235 Test #64: nontetrahedralCatch .................... Passed 0.07 sec test 67 Start 67: depictorCatch 67: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/depictorCatch 67: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor 67: Test timeout computed to be: 1500 63: [15:23:06] w block attempts to set wedging on bond 0 more than once. 63: [15:23:06] improperly formatted w block 63: [15:23:06] atom 3 is not associated with bond 1(1-2) in w block 63: [15:23:06] 63: 63: **** 63: Range Error 63: idx 63: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp 63: Failed Expression: 20 < 20 63: ---------- 63: Stacktrace: 63: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 63: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 63: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 63: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 63: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 63: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 63: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 63: 7# 0x0000AAAAD5BD9B2C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: 8# 0x0000AAAAD5C2D50C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: 9# 0x0000AAAAD5C2DEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: 10# 0x0000AAAAD5C2E2F4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: 11# 0x0000AAAAD5C026B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: 12# 0x0000AAAAD5C02C04 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: 13# 0x0000AAAAD5B95810 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: 14# 0x0000FFFFBC3B229C in /lib/aarch64-linux-gnu/libc.so.6 63: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 63: 16# 0x0000AAAAD5B958F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: ---------- 63: **** 63: 63: [15:23:06] 63: 63: **** 63: Range Error 63: idx 63: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp 63: Failed Expression: 20 < 20 63: ---------- 63: Stacktrace: 63: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 63: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 63: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 63: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 63: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 63: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 63: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 63: 7# 0x0000AAAAD5BD9B2C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: 8# 0x0000AAAAD5C2D50C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: 9# 0x0000AAAAD5C2DEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: 10# 0x0000AAAAD5C2E2F4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: 11# 0x0000AAAAD5C026B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: 12# 0x0000AAAAD5C02C04 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: 13# 0x0000AAAAD5B95810 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: 14# 0x0000FFFFBC3B229C in /lib/aarch64-linux-gnu/libc.so.6 63: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 63: 16# 0x0000AAAAD5B958F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: ---------- 63: **** 63: 63: [15:23:06] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' 63: [15:23:06] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' 63: [15:23:06] SMARTS Parse Error: syntax error while parsing: C1C)foo 63: [15:23:06] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' 63: [15:23:06] SMILES Parse Error: extra close parentheses while parsing: C1C)foo 63: [15:23:06] SMILES Parse Error: check for mistakes around position 4: 63: [15:23:06] C1C)foo 63: [15:23:06] ~~~^ 63: [15:23:06] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' 63: =============================================================================== 63: All tests passed (1584 assertions in 68 test cases) 63: 56/235 Test #63: smiTestCatch ........................... Passed 0.19 sec test 68 Start 68: pyDepictor 68: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/Wrap/testDepictor.py" 68: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap 68: Test timeout computed to be: 1500 61: Randomness seeded to: 4130551587 61: Test 61: 61: ShortAtropisomerNoCoords.cxsmi 61: 61: Test 61: 61: ShortAtropisomer.cxsmi 61: 61: Test 61: 61: ShortAtropisomerArom.cxsmi 61: 61: Test 61: 61: AtropManyChirals.cxsmi 61: 61: Test 61: 61: AtropManyChiralsEnhanced.cxsmi 61: 61: Test 61: 61: AtropManyChiralsEnhanced2.cxsmi 61: 61: Test 61: 61: AtropManyChiralsEnhanced3.cxsmi 61: 61: Test 61: 61: AtropManyChiralsEnhanced4.cxsmi 61: 61: Test 61: 61: BMS-986142_3d_chiral.cxsmi 61: 61: Test 61: 61: BMS-986142_3d.cxsmi 61: 61: Test 61: 61: BMS-986142_atrop1.cxsmi 61: 61: Test 61: 61: BMS-986142_atrop2.cxsmi 61: 61: Test 61: 61: BMS-986142_atrop3.cxsmi 61: 61: Test 61: 61: BMS-986142_atrop4.cxsmi 61: 61: Test 61: 61: BMS-986142_atrop5.cxsmi 61: 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: Test 61: 61: BMS-986142_atrop6.cxsmi 61: 61: Test 61: 61: BMS-986142_atropBad1.cxsmi 61: 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 61: Test 61: 61: BMS-986142_atropBad2.cxsmi 61: 61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 65: Randomness seeded to: 4088435139 65: =============================================================================== 65: All tests passed (14 assertions in 2 test cases) 65: 57/235 Test #65: v2smiTestCatch ......................... Passed 0.27 sec test 69 Start 69: testMrvToMol 69: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 69: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse 69: Test timeout computed to be: 1500 61: Test 61: 61: JDQ443_3d.cxsmi 61: 61: Test 61: 61: JDQ443_atrop1.cxsmi 61: 61: Test 61: 61: JDQ443_atrop2.cxsmi 61: 61: Test 61: 61: JDQ443_atrop3.cxsmi 61: 61: Test 61: 61: JDQ443_atrop4.cxsmi 61: 61: Test 61: 61: JDQ443_atropBad1.cxsmi 61: 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 67: Randomness seeded to: 1482599090 67: =============================================================================== 67: All tests passed (580 assertions in 18 test cases) 67: 58/235 Test #67: depictorCatch .......................... Passed 0.30 sec test 70 Start 70: fileParsersTest1 70: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 70: Test timeout computed to be: 1500 61: Test 61: 61: RP-6306_atrop1.cxsmi 61: 61: Test 61: 61: RP-6306_atrop2.cxsmi 61: 61: Test 61: 61: RP-6306_atrop3.cxsmi 61: 61: Test 61: 61: RP-6306_atrop4.cxsmi 61: 61: Test 61: 61: RP-6306_atrop5.cxsmi 61: 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: Test 61: 61: RP-6306_atrop6.cxsmi 61: 61: Test 61: 61: RP-6306_atropBad1.cxsmi 61: 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 61: Test 61: 61: RP-6306_atropBad2.cxsmi 61: 61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 61: Test 61: 61: RP-6306_3d.cxsmi 61: 61: Test 61: 61: Sotorasib_atrop1.cxsmi 61: 61: Test 61: 61: Sotorasib_atrop2.cxsmi 61: 61: Test 61: 61: Sotorasib_atrop3.cxsmi 61: 61: Test 61: 61: Sotorasib_atrop4.cxsmi 61: 61: Test 61: 61: Sotorasib_atrop5.cxsmi 61: 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 66: [15:23:06] Warning: stereochemistry around double bond may be incorrect in depiction. 61: Test 61: 61: Sotorasib_atropBad1.cxsmi 61: 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 61: Test 61: 61: Sotorasib_atropBad2.cxsmi 61: 61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 69: Using new chirality perception 69: Test 69: 69: rxnStereoMarkedCrossed.mrv 69: 69: Test 69: 69: 145323811.mol 69: 69: [15:23:06] unsupported number of radical electrons 5 61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 70: *************************************** 70: *************************************** 70: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 61: Test 61: 61: Sotorasib_3d.cxsmi 61: 61: Test 61: 61: ZM374979_atrop1.cxsmi 61: 61: Test 61: 61: ZM374979_atrop2.cxsmi 61: 61: Test 61: 61: ZM374979_atrop3.cxsmi 61: 61: Test 61: 61: ZM374979_atrop4.cxsmi 61: 61: Test 61: 61: ZM374979_atropBad1.cxsmi 61: 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 59/235 Test #66: testDepictor ........................... Passed 0.60 sec test 71 Start 71: testAtropisomers 71: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers 71: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 71: Test timeout computed to be: 1500 70: [15:23:06] bond with order 0 found on line 7. This is not part of the MDL specification. 71: [15:23:06] ---- Running with POSIX locale ----- 69: Test 69: 69: NewChiralTest.sdf 69: 69: Test 69: 69: NewChiralTest.sdf 69: 69: Test 69: 69: NewChiralTestNoChiral.sdf 69: 69: Test 69: 69: NewChiralTestNoChiral.sdf 69: 69: Test 69: 69: NewChiralTestAllChiral.sdf 69: 69: Test 69: 69: NewChiralTestAllChiral.sdf 69: 69: Test 69: 69: vendor839.sdf 69: 69: Test 69: 69: ProblemShort.mol 69: 69: [15:23:06] For a MultipleSgroup expansion, the matching orphaned bond was not found 69: The multiple sgroup will be ignored 70: [15:23:06] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) 70: [15:23:06] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) 70: [15:23:06] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 61: Test 61: 61: Mrtx1719_3d.cxsmi 61: 61: Test 61: 61: Mrtx1719_atrop1.cxsmi 61: 61: Test 61: 61: Mrtx1719_atrop2.cxsmi 61: 61: Test 61: 61: Mrtx1719_atrop3.cxsmi 61: 61: Test 61: 61: Mrtx1719_atrop4.cxsmi 61: 61: Test 61: 61: Mrtx1719_atropBad1.cxsmi 61: 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70: generating smiles 70: 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 70: converting back 70: check isomorphism 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 71: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 71: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 71: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 71: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 71: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 71: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 71: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 71: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 71: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 68: ..............[15:23:07] SMILES Parse Error: syntax error while parsing: invalidsmiles 68: [15:23:07] SMILES Parse Error: check for mistakes around position 1: 68: [15:23:07] invalidsmiles 68: [15:23:07] ^ 68: [15:23:07] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' 71: [15:23:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [15:23:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: Atropisomers- 1 hits 3 misses 71: Final results: 71: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses 60/235 Test #71: testAtropisomers ....................... Passed 0.73 sec test 72 Start 72: testSquiggleDoubleBonds 72: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds 72: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 72: Test timeout computed to be: 1500 72: Randomness seeded to: 881995519 72: =============================================================================== 72: All tests passed (15 assertions in 3 test cases) 72: 61/235 Test #72: testSquiggleDoubleBonds ................ Passed 0.04 sec test 73 Start 73: testMolSupplier 73: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 73: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 73: Test timeout computed to be: 1500 68: ..... 68: ---------------------------------------------------------------------- 68: Ran 19 tests in 0.839s 68: 68: OK 73: [15:23:07] 73: ----------------------------------------- 69: Test 69: 69: badWedgeError.sdf 69: 69: Test 69: 69: CrossedDoubleBondWithChiralNbr2.sdf 69: 69: Test 69: 69: CrossedDoubleBondWithChiralNbr.sdf 69: 69: Test 69: 69: SimpleWiggleDoubleBond.sdf 69: 69: Test 69: 69: lostStereoAnd.sdf 69: 69: Test 69: 69: DoubleBondChain.sdf 69: 69: Test 69: 69: UnitsError.sdf 69: 69: Test 69: 69: StarAtom.sdf 69: 69: Test 69: 69: nonProprietary.mol 69: 69: Test 69: 69: ChiralTest.sdf 69: 69: Test 69: 69: TestBond1.mol 69: 69: Test 69: 69: Sgroup_MUL_ParentInMiddle.sdf 69: 69: Test 69: 69: BadRxn.rxn 69: 69: Test 69: 69: FalseChiral.mrv 69: 69: Test 69: 69: FalseChiral.mrv 69: 69: Test 69: 69: Cubane.mrv 69: 69: Test 69: 69: NewChiralTest.mrv 69: 69: Test 69: 69: NewChiralTest.mrv 69: 69: Test 69: 69: NewChiralTestNoChiral.mrv 69: 69: Test 69: 69: NewChiralTestNoChiral.mrv 69: 69: Test 69: 69: NewChiralTestAllChiral.mrv 69: 69: Test 69: 69: NewChiralTestAllChiral.mrv 69: 69: Test 69: 69: DataSgroupMissingUnitsDisplayed.mrv 69: 69: Test 69: 69: lostStereoAnd.mrv 69: 69: Test 69: 69: DoubleBondChain.mrv 69: 69: Test 69: 69: WigglyAndCrossed.mrv 69: 69: Test 69: 69: BondTypes.mrv 69: 69: Test 69: 69: EmbeddedSGroupSUP_MUL.mrv 69: 69: Test 69: 69: EmbeddedSgroupCOP_SUP.mrv 69: 69: Test 69: 69: EmbeddedSgroupDAT_SUP.mrv 69: 69: Test 69: 69: EmbeddedSgroupMULTICENTER_SUP.mrv 69: 69: Test 69: 69: EmbeddedSgroupMUL_MUL.mrv 69: 69: Test 69: 69: EmbeddedSgroupMUL_MUL2.mrv 69: 69: Test 69: 69: EmbeddedSgroupMUL_SUP.mrv 69: 69: Test 69: 69: EmbeddedSgroupSRU_SUP.mrv 69: 69: Test 69: 69: EmbeddedSgroupSUPEXP_SUP.mrv 69: 69: Test 69: 69: EmbeddedSgroupSUPEXP_SUP2.mrv 69: 69: Test 69: 69: EmbeddedSgroupSUP_MULTICENTER.mrv 69: 69: Test 69: 69: EmbeddedSgroupSUP_SUP.mrv 69: 69: Test 69: 69: EmbeddedSgroupSUP_SUP2.mrv 69: 69: Test 69: 69: RgroupBad.mrv 69: 69: Test 69: 69: valenceLessThanDrawn.mrv 69: 69: Test 69: 69: data_sgroup_no_fieldname.mrv 69: 69: Test 69: 69: data_sgroup_empty_field_data.mrv 69: 69: Test 69: 69: radical_value.mrv 69: 69: Test 69: 69: emptyOneLineAtomList.mrv 69: 69: Test 69: 69: mrvValence_value.mrv 69: 69: Test 69: 69: ChiralTest2.mrv 69: 69: Test 69: 69: ChiralTest.mrv 69: 69: Test 69: 69: SnCl2.mrv 69: 69: Test 69: 69: SnH2Cl2.mrv 69: 69: Test 69: 69: marvin01.mrv 69: 69: Test 69: 69: marvin02.mrv 69: 69: Test 69: 69: marvin07.mrv 69: 69: Test 69: 69: marvin10.mrv 69: 69: Test 69: 69: marvin06.mrv 69: 69: Test 69: 69: marvin12.mrv 69: 69: Test 69: 69: EmptyMol.mrv 69: 69: Test 69: 69: Sparse.mrv 69: 69: Test 69: 69: Sparse2.mrv 69: 69: Test 69: 69: Sparse3.mrv 69: 69: Test 69: 69: MarvinNoCoords.mrv 69: 69: Test 69: 69: aspirin.mrv 69: 69: Test 69: 69: MarvinStereoGroupsZeros.mrv 69: 69: Test 69: 69: MarvinStereoGroupsAbs.mrv 69: 69: Test 69: 69: triphenylphosphine.mrv 69: 69: Test 69: 69: MarvinOldSuperGroupTest.mrv 69: 69: Test 69: 69: RadicalTests.mrv 69: 69: Test 69: 69: AnyBond.mrv 69: 69: Test 69: 69: cisBenzene.mrv 69: 69: Test 69: 69: DativeBond.mrv 69: 69: Test 69: 69: MultipleSgroup.mrv 69: 69: Test 69: 69: SgroupExpanded.mrv 69: 69: Test 69: 69: SgroupMultAttach.mrv 69: 69: Test 69: 69: MarvinMissingX2.mrv 69: 69: Test 69: 69: MarvinMissingY2.mrv 69: 69: Test 69: 69: DataSgroup.mrv 69: 69: Test 69: 69: MulticenterSgroup.mrv 69: 69: [15:23:07] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 69: [15:23:07] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 69: Test 69: 69: GenericSgroup.mrv 69: 69: Test 69: 69: MonomerSgroup.mrv 69: 69: Test 69: 69: modification_sgroup.mrv 69: 69: Test 69: 69: copolymer_sgroup.mrv 69: 69: Test 69: 69: MultipleSgroupParentInMiddleOfAtomBlock.mrv 69: 69: Test 69: 69: EmbeddedSgroups.mrv 69: 69: Test 69: 69: marvin03.mrv 69: 69: Test 69: 69: MarvinBadMissingMolID.mrv 69: 69: [15:23:07] 69: 69: **** 69: Test Assert 69: Expression Failed: 69: Violation occurred on line 329 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp 69: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr 69: ---------- 69: Stacktrace: 69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 69: 2# 0x0000AAAAB028AC5C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 69: 3# 0x0000AAAAB0295D5C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 69: 4# 0x0000AAAAB0284918 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 69: 5# 0x0000FFFFA7C0229C in /lib/aarch64-linux-gnu/libc.so.6 69: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 69: 7# 0x0000AAAAB0284B70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 69: ---------- 69: **** 69: 69: Test 69: 69: MarvinBadMissingAtomID.mrv 69: 69: Expected id, elementType for an atom definition in MRV file 69: Test 69: 69: MarvinBadX2.mrv 69: 69: The values x2 and y2 must be large floats in MRV file 69: Test 69: 69: MarvinBadY2.mrv 69: 69: The values x2 and y2 must be large floats in MRV file 69: Test 69: 69: MarvinBadStereoGroupsAbs.mrv 69: 69: Unrecognized group definition 69: Test 69: 69: MarvinBadElementType.mrv 69: 69: Test 69: 69: MarvinBadMissingBondID.mrv 69: 69: Test 69: 69: MarvinBadMissingBondAtomRefs 69: 69: Test 69: 69: MarvinBadMissingBondOrder.mrv 69: 69: bond must have one of: order, queryType, or convention in MRV File 69: Test 69: 69: MarvinBadMissingSruMolID.mrv 69: 69: Expected a molID in MRV file 69: Test 69: 69: MarvinBadMissingSruID.mrv 69: 69: Test 69: 69: MarvinBadMissingSruRole.mrv 69: 69: Test 69: 69: MarvinBadMissingSruAtomRef.mrv 69: 69: Test 69: 69: MarvinBadMissingSruTitle.mrv 69: 69: Test 69: 69: MarvinBadSruAtomRef.mrv 69: 69: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent 69: Test 69: 69: MarvinBadSruID.mrv 69: 69: Test 69: 69: MarvinBadSruRole.mrv 69: 69: Test 69: 69: MarvinBadSruAtomRef.mrv 69: 69: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent 69: Test 69: 69: MarvinBadSruAtomRef.mrv 69: 69: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent 69: Test 69: 69: MarvinBadSruConnect.mrv 69: 69: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file 69: Test 69: 69: MarvinBadSupAttachAtom.mrv 69: 69: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 69: Test 69: 69: MarvinBadSupAttachBond.mrv 69: 69: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file 69: Test 69: 69: MarvinBadSupAttachOrder.mrv 69: 69: Order for an AttachmentPoint definition must be an integer in MRV file 69: Test 69: 69: MarvinBadSupAttachAtom.mrv 69: 69: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 69: Test 69: 69: MarvinBadSupAttachAtom.mrv 69: 69: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 69: Test 69: 69: MarvinBadSupAttachAtom.mrv 69: 69: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 69: Test 69: 69: MarvinBadSupMissingAttachBond.mrv 69: 69: No attachment point found for bond to the condensed atom in a superatomSgroup 69: Test 69: 69: MarvinBadSupMissingAttachOrder.mrv 69: 69: Expected atom, order and bond, for an AttachmentPoint definition in MRV file 73: [15:23:07] 73: 73: **** 73: Invariant Violation 73: bad prop value 73: Violation occurred on line 155 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 73: Failed Expression: nSwaps < 2 73: ---------- 73: Stacktrace: 73: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 73: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 73: 2# 0x0000FFFF94575C7C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 73: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 73: 4# 0x0000AAAAC0E9D59C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 73: 5# 0x0000AAAAC0E92A68 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 73: 6# 0x0000AAAAC0E60E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 73: 7# 0x0000FFFF93B7229C in /lib/aarch64-linux-gnu/libc.so.6 73: 8# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 73: 9# 0x0000AAAAC0E627F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 73: ---------- 73: **** 73: 62/235 Test #68: pyDepictor ............................. Passed 1.50 sec test 74 Start 74: testGeneralFileReader 74: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader 74: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 74: Test timeout computed to be: 1500 74: [15:23:07] 74: ----------------------------------------- 74: [15:23:07] Finished: testDetermineFormat() 74: [15:23:07] ----------------------------------------- 74: 74: [15:23:07] 74: ----------------------------------------- 69: Test 69: 69: marvin03.mrv 69: 69: Test 69: 69: Cubane.mrv 69: 69: Test 69: 69: FalseAtropisomer.mrv 69: 69: Test 69: 69: AtropEnhancedStereo.mrv 69: 69: Test 69: 69: AtropManyChirals.mrv 69: 69: Test 69: 69: AtropManyChiralsEnhanced.mrv 69: 69: Test 69: 69: AtropManyChiralsEnhanced2.mrv 69: 69: Test 69: 69: AtropManyChiralsEnhanced3.mrv 69: 69: Test 69: 69: AtropManyChiralsEnhanced4.mrv 69: 69: Test 69: 69: BMS-986142_3d_chiral.mrv 69: 69: Test 69: 69: BMS-986142_3d.mrv 69: 69: Test 69: 69: BMS-986142_atrop1.mrv 69: 69: Test 69: 69: BMS-986142_atrop2.mrv 69: 69: Test 69: 69: BMS-986142_atrop3.mrv 69: 69: Test 69: 69: BMS-986142_atrop4.mrv 69: 69: Test 69: 69: BMS-986142_atrop5.mrv 69: 69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 73: [15:23:07] Finished: testMolSup() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] Finished: testRandMolSup() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 69: Test 69: 69: BMS-986142_atrop6.mrv 69: 69: Test 69: 69: BMS-986142_atrop7.mrv 69: 69: Test 69: 69: BMS-986142_atrop8.mrv 69: 69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: Test 69: 69: BMS-986142_atropBad2.mrv 69: 69: [15:23:07] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 74: [15:23:07] Finished: testSdf() 74: [15:23:07] ----------------------------------------- 74: 74: [15:23:07] 74: ----------------------------------------- 73: [15:23:07] Finished: testSmilesSup() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] ------------------------------------------------------ 73: [15:23:07] SMILES Parse Error: syntax error while parsing: fail 73: [15:23:07] SMILES Parse Error: check for mistakes around position 1: 73: [15:23:07] fail 73: [15:23:07] ^ 73: [15:23:07] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' 73: [15:23:07] ERROR: Smiles parse error on line 3 73: [15:23:07] ERROR: Cannot create molecule from : 'fail' 73: [15:23:07] ------------------------------------------------------ 73: [15:23:07] ------------------------------------------------------ 73: [15:23:07] >>> This may result in an infinite loop. It should finish almost immediately: 73: [15:23:07] <<< done. 73: [15:23:07] Finished: testSmilesSupFromText() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 74: [15:23:07] Finished: testSmi() 74: [15:23:07] ----------------------------------------- 74: 74: [15:23:07] 74: ----------------------------------------- 73: [15:23:07] Finished: testSmilesWriter() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 69: Test 69: 69: JDQ443_3d.mrv 69: 69: Test 69: 69: JDQ443_atrop1.mrv 69: 69: Test 69: 69: JDQ443_atrop2.mrv 69: 69: Test 69: 69: JDQ443_atrop3.mrv 69: 69: Test 69: 69: JDQ443_atropBad1.mrv 69: 69: [15:23:07] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 73: [15:23:07] Finished: testSDWriter() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] Finished: testSDSupplierEnding() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] Finished: testSuppliersEmptyFile() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] Finished: testCisTrans() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] Finished: testStereoRound() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 73: [15:23:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 73: [15:23:07] Finished: testIssue226() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] Finished: testTDTSupplier1() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] Finished: testTDTSupplier2() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] Finished: testTDTSupplier3() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] Finished: testSDSupplierFromText() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] ERROR: Problems encountered parsing data fields 73: [15:23:07] ERROR: moving to the beginning of the next molecule 73: [15:23:07] ERROR: Problems encountered parsing data fields 73: [15:23:07] ERROR: moving to the beginning of the next molecule 73: [15:23:07] Spurious data before the first property will be ignored 73: [15:23:07] Property will be truncated after the first blank line 73: [15:23:07] Property will be truncated after the first blank line 73: [15:23:07] Property will be truncated after the first blank line 73: [15:23:07] Finished: testSDSupplierStrLax1() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] ERROR: Problems encountered parsing data fields 73: [15:23:07] ERROR: moving to the beginning of the next molecule 73: [15:23:07] Property will be truncated after the first blank line 73: [15:23:07] Finished: testSDSupplierStrLax2() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] ERROR: Problems encountered parsing data fields 73: [15:23:07] ERROR: moving to the beginning of the next molecule 73: [15:23:07] ERROR: Problems encountered parsing data fields 73: [15:23:07] ERROR: moving to the beginning of the next molecule 73: [15:23:07] Spurious data before the first property will be ignored 73: [15:23:07] Property will be truncated after the first blank line 73: [15:23:07] Property will be truncated after the first blank line 73: [15:23:07] Property will be truncated after the first blank line 73: [15:23:07] Finished: testSDSupplierFromTextStrLax1() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] ERROR: Problems encountered parsing data fields 73: [15:23:07] ERROR: moving to the beginning of the next molecule 73: [15:23:07] Property will be truncated after the first blank line 73: [15:23:07] Finished: testSDSupplierFromTextStrLax2() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] Finished: testIssue265() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] ERROR: End of data field name not found 73: [15:23:07] ERROR: moving to the beginning of the next molecule 73: [15:23:07] Explicit valence for atom # 0 F, 2, is greater than permitted 73: [15:23:07] ERROR: Could not sanitize molecule ending on line 16 73: [15:23:07] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted 73: [15:23:07] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 73: [15:23:07] ERROR: moving to the beginning of the next molecule 73: [15:23:07] ERROR: Bond line too short: 'M END' on line 18 73: [15:23:07] ERROR: moving to the beginning of the next molecule 73: [15:23:07] Finished: testSDErrorHandling() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 69: Test 69: 69: RP-6306_atrop1.mrv 69: 69: Test 69: 69: RP-6306_atrop2.mrv 69: 69: Test 69: 69: RP-6306_atrop3.mrv 69: 69: Test 69: 69: RP-6306_atrop4.mrv 69: 69: Test 69: 69: RP-6306_atrop5.mrv 69: 69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 73: [15:23:07] Finished: testIssue381() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 74: [15:23:07] Finished: testMae() 74: [15:23:07] ----------------------------------------- 74: 74: [15:23:07] 74: ----------------------------------------- 74: [15:23:07] Finished: testTdt() 74: [15:23:07] ----------------------------------------- 74: 69: Test 69: 69: RP-6306_atropBad1.mrv 69: 69: [15:23:07] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 73: [15:23:07] Finished: testSetStreamIndices() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 63/235 Test #74: testGeneralFileReader .................. Passed 0.28 sec test 75 Start 75: testMultithreadedMolSupplier 75: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier 75: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 75: Test timeout computed to be: 1500 69: Test 69: 69: RP-6306_atropBad2.mrv 69: 69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: [15:23:07] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 73: [15:23:07] Finished: testMixIterAndRandom() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: build: 73: [15:23:07] Finished: testRemoveHs() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] Finished: testGetItemText() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] Finished: testForwardSDSupplier() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] Finished: testMissingCRSDSupplier() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] Finished: testIssue3482695() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] ERROR: Cannot convert 'foo' to unsigned int on line 557 73: [15:23:07] ERROR: moving to the beginning of the next molecule 75: [15:23:07] 75: ----------------------------------------- 73: [15:23:07] Finished: testIssue3525673() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] Finished: testBlankLinesInProps() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] Finished: testSkipLines() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] Finished: testGitHub23() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 69: Test 69: 69: RP-6306_3d.mrv 69: 69: Test 69: 69: Sotorasib_atrop1.mrv 69: 69: Test 69: 69: Sotorasib_atrop2.mrv 69: 69: Test 69: 69: Sotorasib_atrop3.mrv 69: 69: Test 69: 69: Sotorasib_atrop4.mrv 69: 69: Test 69: 69: Sotorasib_atrop5.mrv 69: 69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 73: [15:23:07] Finished: testGitHub88() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 69: Test 69: 69: Sotorasib_atropBad1.mrv 69: 69: [15:23:07] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 69: Test 69: 69: Sotorasib_atropBad2.mrv 69: 69: [15:23:07] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 73: [15:23:07] Finished: testGitHub2285() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 73: [15:23:07] ERROR: Smiles parse error on line 1 73: [15:23:07] ERROR: Cannot create molecule from : 'c1ccccc' 73: [15:23:07] SMILES Parse Error: extra open parentheses while parsing: C(C 73: [15:23:07] SMILES Parse Error: check for mistakes around position 2: 73: [15:23:07] C(C 73: [15:23:07] ~^ 73: [15:23:07] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' 73: [15:23:07] ERROR: Smiles parse error on line 3 73: [15:23:07] ERROR: Cannot create molecule from : 'C(C' 73: [15:23:07] Explicit valence for atom # 1 C, 5, is greater than permitted 73: [15:23:07] ERROR: Could not sanitize molecule on line 5 73: [15:23:07] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted 73: [15:23:07] Explicit valence for atom # 1 F, 2, is greater than permitted 73: [15:23:07] ERROR: Could not sanitize molecule ending on line 21 73: [15:23:07] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 73: [15:23:07] Explicit valence for atom # 1 F, 2, is greater than permitted 73: [15:23:07] ERROR: Could not sanitize molecule ending on line 21 73: [15:23:07] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 73: [15:23:07] Explicit valence for atom # 1 F, 2, is greater than permitted 73: [15:23:07] ERROR: Could not sanitize molecule ending on line 21 73: [15:23:07] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 73: [15:23:07] ERROR: Atom line too short: ' -9.6' on line 28 73: [15:23:07] ERROR: moving to the beginning of the next molecule 73: [15:23:07] Explicit valence for atom # 1 F, 2, is greater than permitted 73: [15:23:07] ERROR: Could not sanitize molecule ending on line 21 73: [15:23:07] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 73: [15:23:07] ERROR: Atom line too short: ' -9.6' on line 28 73: [15:23:07] ERROR: moving to the beginning of the next molecule 73: [15:23:07] Finished: testGitHub2479() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] 73: 73: **** 73: Invariant Violation 73: bad chiral bond 73: Violation occurred on line 161 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 73: Failed Expression: bnd 73: ---------- 73: Stacktrace: 73: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 73: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 73: 2# 0x0000FFFF945761A4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 73: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 73: 4# 0x0000AAAAC0E636A0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 73: 5# 0x0000AAAAC0E62514 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 73: 6# 0x0000FFFF93B7229C in /lib/aarch64-linux-gnu/libc.so.6 73: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 73: 8# 0x0000AAAAC0E627F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 73: ---------- 73: **** 73: 73: [15:23:07] Finished: testGitHub2881() 73: [15:23:07] ----------------------------------------- 73: 73: [15:23:07] ----------------------------------------- 73: [15:23:07] Finished: testGitHub3517() 73: [15:23:07] ----------------------------------------- 73: 64/235 Test #73: testMolSupplier ........................ Passed 0.62 sec test 76 Start 76: testMolWriter 76: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter 76: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 76: Test timeout computed to be: 1500 61: Test 61: 61: AtropCanon1.cxsmi 61: 61: Test 61: 61: AtropCanon2.cxsmi 61: 61: Test 61: 61: AtropCanon3.cxsmi 61: 61: Test 61: 61: BMS-986142_3d_chiral.cxsmi 61: 61: Test 61: 61: BMS-986142_3d.cxsmi 61: 61: =============================================================================== 61: All tests passed (2445 assertions in 29 test cases) 61: 65/235 Test #61: cxsmilesTest ........................... Passed 2.21 sec test 77 Start 77: testTplParser 77: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testTplParser 77: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 77: Test timeout computed to be: 1500 69: Test 69: 69: Sotorasib_3d.mrv 69: 69: Test 69: 69: ZM374979_atrop1.mrv 69: 69: Test 69: 69: ZM374979_atrop2.mrv 69: 69: Test 69: 69: ZM374979_atrop3.mrv 69: 69: Test 69: 69: ZM374979_atropBad1.mrv 69: 69: [15:23:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 70: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 70: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 70: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 70: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 70: [15:23:08] deprecated group abbreviation ignored on line 24 70: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] 70: [15:23:08] 70: 70: **** 70: Post-condition Violation 70: Element 'Mv' not found 70: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 70: Failed Expression: anum > -1 70: ---------- 70: Stacktrace: 70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 70: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 3# 0x0000FFFFB8CA7FE4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 4# 0x0000FFFFB8CB5BC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 5# 0x0000FFFFB8CB6AEC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 9# 0x0000AAAAC525F83C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: 10# 0x0000AAAAC52D4B44 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: 11# 0x0000AAAAC5245CB8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: 12# 0x0000FFFFB837229C in /lib/aarch64-linux-gnu/libc.so.6 70: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 70: 14# 0x0000AAAAC5245EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: ---------- 70: **** 70: 66/235 Test #77: testTplParser .......................... Passed 0.05 sec test 78 Start 78: testMol2ToMol 78: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol 78: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 78: Test timeout computed to be: 1500 69: Test 69: 69: mrtx1719_3d.mrv 69: 69: Test 69: 69: mrtx1719_atrop1.mrv 69: 69: Test 69: 69: mrtx1719_atrop2.mrv 69: 69: Test 69: 69: mrtx1719_atrop3.mrv 69: 69: Test 69: 69: mrtx1719_atropBad1.mrv 69: 69: [15:23:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 67/235 Test #78: testMol2ToMol .......................... Passed 0.08 sec test 79 Start 79: testSequence 79: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSequence 79: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 79: Test timeout computed to be: 1500 69: Test 69: 69: FalseAtropisomer.mrv 69: 69: Test 69: 69: AtropEnhancedStereo.mrv 69: 69: Test 69: 69: AtropManyChirals.mrv 69: 69: Test 69: 69: AtropManyChiralsEnhanced.mrv 69: 69: Test 69: 69: AtropManyChiralsEnhanced2.mrv 69: 69: Test 69: 69: AtropManyChiralsEnhanced3.mrv 69: 69: Test 69: 69: AtropManyChiralsEnhanced4.mrv 69: 69: Test 69: 69: BMS-986142_3d_chiral.mrv 69: 69: Test 69: 69: BMS-986142_3d.mrv 69: 69: Test 69: 69: BMS-986142_atrop1.mrv 69: 69: Test 69: 69: BMS-986142_atrop2.mrv 69: 69: Test 69: 69: BMS-986142_atrop3.mrv 69: 69: Test 69: 69: BMS-986142_atrop4.mrv 69: 69: Test 69: 69: BMS-986142_atrop5.mrv 69: 69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 70: [15:23:08] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 70: [15:23:08] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 69: Test 69: 69: BMS-986142_atrop6.mrv 69: 69: Test 69: 69: BMS-986142_atrop7.mrv 69: 69: Test 69: 69: BMS-986142_atrop8.mrv 69: 69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 79: Sequence: GREG 79: HELM: PEPTIDE1{G.R.E.G}$$$$ 79: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O 79: PDB: 79: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 23 OE1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 24 OE2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O 79: CONECT 1 2 79: CONECT 2 3 79: CONECT 3 4 4 5 79: CONECT 5 6 79: CONECT 6 7 9 79: CONECT 7 8 8 16 79: CONECT 9 10 79: CONECT 10 11 79: CONECT 11 12 79: CONECT 12 13 79: CONECT 13 14 14 15 79: CONECT 16 17 79: CONECT 17 18 20 79: CONECT 18 19 19 25 79: CONECT 20 21 79: CONECT 21 22 79: CONECT 22 23 23 24 79: CONECT 25 26 79: CONECT 26 27 79: CONECT 27 28 28 29 79: END 79: 79: Sequence: TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN 79: 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}$$$$ 79: 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 79: PDB: 79: ATOM 1 N THR A 1 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 2 CA THR A 1 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 3 C THR A 1 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 4 O THR A 1 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 5 CB THR A 1 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 6 OG1 THR A 1 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 7 CG2 THR A 1 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 8 N THR A 2 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 9 CA THR A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 10 C THR A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 11 O THR A 2 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 12 CB THR A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 13 OG1 THR A 2 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 14 CG2 THR A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 15 N CYS A 3 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 16 CA CYS A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 17 C CYS A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 18 O CYS A 3 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 19 CB CYS A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 20 SG CYS A 3 0.000 0.000 0.000 1.00 0.00 S 79: ATOM 21 N CYS A 4 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 22 CA CYS A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 23 C CYS A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 24 O CYS A 4 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 25 CB CYS A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 26 SG CYS A 4 0.000 0.000 0.000 1.00 0.00 S 79: ATOM 27 N PRO A 5 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 28 CA PRO A 5 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 29 C PRO A 5 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 30 O PRO A 5 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 31 CB PRO A 5 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 32 CG PRO A 5 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 33 CD PRO A 5 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 34 N SER A 6 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 35 CA SER A 6 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 36 C SER A 6 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 37 O SER A 6 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 38 CB SER A 6 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 39 OG SER A 6 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 40 N ILE A 7 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 41 CA ILE A 7 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 42 C ILE A 7 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 43 O ILE A 7 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 44 CB ILE A 7 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 45 CG1 ILE A 7 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 46 CG2 ILE A 7 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 47 CD1 ILE A 7 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 48 N VAL A 8 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 49 CA VAL A 8 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 50 C VAL A 8 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 51 O VAL A 8 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 52 CB VAL A 8 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 53 CG1 VAL A 8 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 54 CG2 VAL A 8 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 55 N ALA A 9 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 56 CA ALA A 9 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 57 C ALA A 9 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 58 O ALA A 9 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 59 CB ALA A 9 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 60 N ARG A 10 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 61 CA ARG A 10 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 62 C ARG A 10 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 63 O ARG A 10 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 64 CB ARG A 10 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 65 CG ARG A 10 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 66 CD ARG A 10 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 67 NE ARG A 10 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 68 CZ ARG A 10 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 69 NH1 ARG A 10 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 70 NH2 ARG A 10 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 71 N SER A 11 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 72 CA SER A 11 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 73 C SER A 11 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 74 O SER A 11 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 75 CB SER A 11 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 76 OG SER A 11 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 77 N ASN A 12 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 78 CA ASN A 12 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 79 C ASN A 12 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 80 O ASN A 12 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 81 CB ASN A 12 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 82 CG ASN A 12 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 83 OD1 ASN A 12 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 84 ND2 ASN A 12 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 85 N PHE A 13 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 86 CA PHE A 13 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 87 C PHE A 13 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 88 O PHE A 13 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 89 CB PHE A 13 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 90 CG PHE A 13 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 91 CD1 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 92 CD2 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 93 CE1 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 94 CE2 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 95 CZ PHE A 13 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 96 N ASN A 14 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 97 CA ASN A 14 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 98 C ASN A 14 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 99 O ASN A 14 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 100 CB ASN A 14 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 101 CG ASN A 14 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 102 OD1 ASN A 14 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 103 ND2 ASN A 14 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 104 N VAL A 15 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 105 CA VAL A 15 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 106 C VAL A 15 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 107 O VAL A 15 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 108 CB VAL A 15 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 109 CG1 VAL A 15 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 110 CG2 VAL A 15 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 111 N CYS A 16 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 112 CA CYS A 16 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 113 C CYS A 16 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 114 O CYS A 16 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 115 CB CYS A 16 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 116 SG CYS A 16 0.000 0.000 0.000 1.00 0.00 S 79: ATOM 117 N ARG A 17 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 118 CA ARG A 17 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 119 C ARG A 17 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 120 O ARG A 17 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 121 CB ARG A 17 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 122 CG ARG A 17 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 123 CD ARG A 17 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 124 NE ARG A 17 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 125 CZ ARG A 17 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 126 NH1 ARG A 17 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 127 NH2 ARG A 17 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 128 N LEU A 18 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 129 CA LEU A 18 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 130 C LEU A 18 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 131 O LEU A 18 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 132 CB LEU A 18 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 133 CG LEU A 18 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 134 CD1 LEU A 18 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 135 CD2 LEU A 18 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 136 N PRO A 19 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 137 CA PRO A 19 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 138 C PRO A 19 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 139 O PRO A 19 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 140 CB PRO A 19 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 141 CG PRO A 19 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 142 CD PRO A 19 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 143 N GLY A 20 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 144 CA GLY A 20 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 145 C GLY A 20 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 146 O GLY A 20 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 147 N THR A 21 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 148 CA THR A 21 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 149 C THR A 21 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 150 O THR A 21 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 151 CB THR A 21 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 152 OG1 THR A 21 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 153 CG2 THR A 21 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 154 N PRO A 22 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 155 CA PRO A 22 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 156 C PRO A 22 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 157 O PRO A 22 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 158 CB PRO A 22 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 159 CG PRO A 22 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 160 CD PRO A 22 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 161 N GLU A 23 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 162 CA GLU A 23 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 163 C GLU A 23 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 164 O GLU A 23 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 165 CB GLU A 23 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 166 CG GLU A 23 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 167 CD GLU A 23 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 168 OE1 GLU A 23 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 169 OE2 GLU A 23 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 170 N ALA A 24 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 171 CA ALA A 24 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 172 C ALA A 24 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 173 O ALA A 24 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 174 CB ALA A 24 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 175 N ILE A 25 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 176 CA ILE A 25 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 177 C ILE A 25 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 178 O ILE A 25 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 179 CB ILE A 25 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 180 CG1 ILE A 25 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 181 CG2 ILE A 25 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 182 CD1 ILE A 25 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 183 N CYS A 26 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 184 CA CYS A 26 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 185 C CYS A 26 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 186 O CYS A 26 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 187 CB CYS A 26 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 188 SG CYS A 26 0.000 0.000 0.000 1.00 0.00 S 79: ATOM 189 N ALA A 27 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 190 CA ALA A 27 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 191 C ALA A 27 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 192 O ALA A 27 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 193 CB ALA A 27 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 194 N THR A 28 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 195 CA THR A 28 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 196 C THR A 28 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 197 O THR A 28 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 198 CB THR A 28 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 199 OG1 THR A 28 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 200 CG2 THR A 28 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 201 N TYR A 29 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 202 CA TYR A 29 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 203 C TYR A 29 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 204 O TYR A 29 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 205 CB TYR A 29 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 206 CG TYR A 29 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 207 CD1 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 208 CD2 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 209 CE1 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 210 CE2 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 211 CZ TYR A 29 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 212 OH TYR A 29 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 213 N THR A 30 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 214 CA THR A 30 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 215 C THR A 30 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 216 O THR A 30 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 217 CB THR A 30 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 218 OG1 THR A 30 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 219 CG2 THR A 30 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 220 N GLY A 31 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 221 CA GLY A 31 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 222 C GLY A 31 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 223 O GLY A 31 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 224 N CYS A 32 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 225 CA CYS A 32 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 226 C CYS A 32 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 227 O CYS A 32 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 228 CB CYS A 32 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 229 SG CYS A 32 0.000 0.000 0.000 1.00 0.00 S 79: ATOM 230 N ILE A 33 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 231 CA ILE A 33 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 232 C ILE A 33 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 233 O ILE A 33 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 234 CB ILE A 33 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 235 CG1 ILE A 33 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 236 CG2 ILE A 33 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 237 CD1 ILE A 33 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 238 N ILE A 34 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 239 CA ILE A 34 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 240 C ILE A 34 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 241 O ILE A 34 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 242 CB ILE A 34 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 243 CG1 ILE A 34 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 244 CG2 ILE A 34 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 245 CD1 ILE A 34 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 246 N ILE A 35 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 247 CA ILE A 35 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 248 C ILE A 35 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 249 O ILE A 35 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 250 CB ILE A 35 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 251 CG1 ILE A 35 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 252 CG2 ILE A 35 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 253 CD1 ILE A 35 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 254 N PRO A 36 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 255 CA PRO A 36 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 256 C PRO A 36 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 257 O PRO A 36 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 258 CB PRO A 36 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 259 CG PRO A 36 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 260 CD PRO A 36 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 261 N GLY A 37 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 262 CA GLY A 37 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 263 C GLY A 37 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 264 O GLY A 37 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 265 N ALA A 38 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 266 CA ALA A 38 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 267 C ALA A 38 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 268 O ALA A 38 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 269 CB ALA A 38 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 270 N THR A 39 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 271 CA THR A 39 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 272 C THR A 39 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 273 O THR A 39 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 274 CB THR A 39 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 275 OG1 THR A 39 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 276 CG2 THR A 39 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 277 N CYS A 40 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 278 CA CYS A 40 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 279 C CYS A 40 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 280 O CYS A 40 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 281 CB CYS A 40 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 282 SG CYS A 40 0.000 0.000 0.000 1.00 0.00 S 79: ATOM 283 N PRO A 41 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 284 CA PRO A 41 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 285 C PRO A 41 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 286 O PRO A 41 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 287 CB PRO A 41 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 288 CG PRO A 41 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 289 CD PRO A 41 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 290 N GLY A 42 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 291 CA GLY A 42 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 292 C GLY A 42 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 293 O GLY A 42 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 294 N ASP A 43 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 295 CA ASP A 43 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 296 C ASP A 43 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 297 O ASP A 43 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 298 CB ASP A 43 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 299 CG ASP A 43 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 300 OD1 ASP A 43 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 301 OD2 ASP A 43 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 302 N TYR A 44 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 303 CA TYR A 44 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 304 C TYR A 44 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 305 O TYR A 44 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 306 CB TYR A 44 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 307 CG TYR A 44 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 308 CD1 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 309 CD2 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 310 CE1 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 311 CE2 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 312 CZ TYR A 44 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 313 OH TYR A 44 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 314 N ALA A 45 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 315 CA ALA A 45 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 316 C ALA A 45 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 317 O ALA A 45 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 318 CB ALA A 45 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 319 N ASN A 46 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 320 CA ASN A 46 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 321 C ASN A 46 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 322 O ASN A 46 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 323 CB ASN A 46 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 324 CG ASN A 46 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 325 OD1 ASN A 46 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 326 ND2 ASN A 46 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 327 OXT ASN A 46 0.000 0.000 0.000 1.00 0.00 O 79: CONECT 1 2 79: CONECT 2 3 5 79: CONECT 3 4 4 8 79: CONECT 5 6 7 79: CONECT 8 9 79: CONECT 9 10 12 79: CONECT 10 11 11 15 79: CONECT 12 13 14 79: CONECT 15 16 79: CONECT 16 17 19 79: CONECT 17 18 18 21 79: CONECT 19 20 79: CONECT 21 22 79: CONECT 22 23 25 79: CONECT 23 24 24 27 79: CONECT 25 26 79: CONECT 27 28 33 79: CONECT 28 29 31 79: CONECT 29 30 30 34 79: CONECT 31 32 79: CONECT 32 33 79: CONECT 34 35 79: CONECT 35 36 38 79: CONECT 36 37 37 40 79: CONECT 38 39 79: CONECT 40 41 79: CONECT 41 42 44 79: CONECT 42 43 43 48 79: CONECT 44 45 46 79: CONECT 46 47 79: CONECT 48 49 79: CONECT 49 50 52 79: CONECT 50 51 51 55 79: CONECT 52 53 54 79: CONECT 55 56 79: CONECT 56 57 59 79: CONECT 57 58 58 60 79: CONECT 60 61 79: CONECT 61 62 64 79: CONECT 62 63 63 71 79: CONECT 64 65 79: CONECT 65 66 79: CONECT 66 67 79: CONECT 67 68 79: CONECT 68 69 69 70 79: CONECT 71 72 79: CONECT 72 73 75 79: CONECT 73 74 74 77 79: CONECT 75 76 79: CONECT 77 78 79: CONECT 78 79 81 79: CONECT 79 80 80 85 79: CONECT 81 82 79: CONECT 82 83 83 84 79: CONECT 85 86 79: CONECT 86 87 89 79: CONECT 87 88 88 96 79: CONECT 89 90 79: CONECT 90 91 91 92 79: CONECT 91 93 79: CONECT 92 94 94 79: CONECT 93 95 95 79: CONECT 94 95 79: CONECT 96 97 79: CONECT 97 98 100 79: CONECT 98 99 99 104 79: CONECT 100 101 79: CONECT 101 102 102 103 79: CONECT 104 105 79: CONECT 105 106 108 79: CONECT 106 107 107 111 79: CONECT 108 109 110 79: CONECT 111 112 79: CONECT 112 113 115 79: CONECT 113 114 114 117 79: CONECT 115 116 79: CONECT 117 118 79: CONECT 118 119 121 79: CONECT 119 120 120 128 79: CONECT 121 122 79: CONECT 122 123 79: CONECT 123 124 79: CONECT 124 125 79: CONECT 125 126 126 127 79: CONECT 128 129 79: CONECT 129 130 132 79: CONECT 130 131 131 136 79: CONECT 132 133 79: CONECT 133 134 135 79: CONECT 136 137 142 79: CONECT 137 138 140 79: CONECT 138 139 139 143 79: CONECT 140 141 79: CONECT 141 142 79: CONECT 143 144 79: CONECT 144 145 79: CONECT 145 146 146 147 79: CONECT 147 148 79: CONECT 148 149 151 79: CONECT 149 150 150 154 79: CONECT 151 152 153 79: CONECT 154 155 160 79: CONECT 155 156 158 79: CONECT 156 157 157 161 79: CONECT 158 159 79: CONECT 159 160 79: CONECT 161 162 79: CONECT 162 163 165 79: CONECT 163 164 164 170 79: CONECT 165 166 79: CONECT 166 167 79: CONECT 167 168 168 169 79: CONECT 170 171 79: CONECT 171 172 174 79: CONECT 172 173 173 175 79: CONECT 175 176 79: CONECT 176 177 179 79: CONECT 177 178 178 183 79: CONECT 179 180 181 79: CONECT 181 182 79: CONECT 183 184 79: CONECT 184 185 187 79: CONECT 185 186 186 189 79: CONECT 187 188 79: CONECT 189 190 79: CONECT 190 191 193 79: CONECT 191 192 192 194 79: CONECT 194 195 79: CONECT 195 196 198 79: CONECT 196 197 197 201 79: CONECT 198 199 200 79: CONECT 201 202 79: CONECT 202 203 205 79: CONECT 203 204 204 213 79: CONECT 205 206 79: CONECT 206 207 207 208 79: CONECT 207 209 79: CONECT 208 210 210 79: CONECT 209 211 211 79: CONECT 210 211 79: CONECT 211 212 79: CONECT 213 214 79: CONECT 214 215 217 79: CONECT 215 216 216 220 79: CONECT 217 218 219 79: CONECT 220 221 79: CONECT 221 222 79: CONECT 222 223 223 224 79: CONECT 224 225 79: CONECT 225 226 228 79: CONECT 226 227 227 230 79: CONECT 228 229 79: CONECT 230 231 79: CONECT 231 232 234 79: CONECT 232 233 233 238 79: CONECT 234 235 236 79: CONECT 236 237 79: CONECT 238 239 79: CONECT 239 240 242 79: CONECT 240 241 241 246 79: CONECT 242 243 244 79: CONECT 244 245 79: CONECT 246 247 79: CONECT 247 248 250 79: CONECT 248 249 249 254 79: CONECT 250 251 252 79: CONECT 252 253 79: CONECT 254 255 260 79: CONECT 255 256 258 79: CONECT 256 257 257 261 79: CONECT 258 259 79: CONECT 259 260 79: CONECT 261 262 79: CONECT 262 263 79: CONECT 263 264 264 265 79: CONECT 265 266 79: CONECT 266 267 269 79: CONECT 267 268 268 270 79: CONECT 270 271 79: CONECT 271 272 274 79: CONECT 272 273 273 277 79: CONECT 274 275 276 79: CONECT 277 278 79: CONECT 278 279 281 79: CONECT 279 280 280 283 79: CONECT 281 282 79: CONECT 283 284 289 79: CONECT 284 285 287 79: CONECT 285 286 286 290 79: CONECT 287 288 79: CONECT 288 289 79: CONECT 290 291 79: CONECT 291 292 79: CONECT 292 293 293 294 79: CONECT 294 295 79: CONECT 295 296 298 79: CONECT 296 297 297 302 79: CONECT 298 299 79: CONECT 299 300 300 301 79: CONECT 302 303 79: CONECT 303 304 306 79: CONECT 304 305 305 314 79: CONECT 306 307 79: CONECT 307 308 308 309 79: CONECT 308 310 79: CONECT 309 311 311 79: CONECT 310 312 312 79: CONECT 311 312 79: CONECT 312 313 79: CONECT 314 315 79: CONECT 315 316 318 79: CONECT 316 317 317 319 79: CONECT 319 320 79: CONECT 320 321 323 79: CONECT 321 322 322 327 79: CONECT 323 324 79: CONECT 324 325 325 326 79: END 79: 79: Sequence: GREG 79: HELM: PEPTIDE1{G.R.E.G}$$$$ 79: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O 79: PDB: 79: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 23 OE1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 24 OE2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O 79: CONECT 1 2 79: CONECT 2 3 79: CONECT 3 4 4 5 79: CONECT 5 6 79: CONECT 6 7 9 79: CONECT 7 8 8 16 79: CONECT 9 10 79: CONECT 10 11 79: CONECT 11 12 79: CONECT 12 13 79: CONECT 13 14 14 15 79: CONECT 16 17 79: CONECT 17 18 20 79: CONECT 18 19 19 25 79: CONECT 20 21 79: CONECT 21 22 79: CONECT 22 23 23 24 79: CONECT 25 26 79: CONECT 26 27 79: CONECT 27 28 28 29 79: END 79: 79: Sequence: CYIQNCPLG 79: HELM: PEPTIDE1{C.Y.I.Q.N.C.P.L.G.[am]}$PEPTIDE1,PEPTIDE1,1:R3-6:R3$$$ 79: 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 79: PDB: 79: ATOM 1 N CYS A 1 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 2 CA CYS A 1 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 3 C CYS A 1 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 4 O CYS A 1 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 5 CB CYS A 1 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 6 SG CYS A 1 0.000 0.000 0.000 1.00 0.00 S 79: ATOM 7 N TYR A 2 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 8 CA TYR A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 9 C TYR A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 10 O TYR A 2 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 11 CB TYR A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 12 CG TYR A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 13 CD1 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 14 CD2 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 15 CE1 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 16 CE2 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 17 CZ TYR A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 18 OH TYR A 2 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 19 N ILE A 3 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 20 CA ILE A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 21 C ILE A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 22 O ILE A 3 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 23 CB ILE A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 24 CG1 ILE A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 25 CG2 ILE A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 26 CD1 ILE A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 27 N GLN A 4 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 28 CA GLN A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 29 C GLN A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 30 O GLN A 4 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 31 CB GLN A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 32 CG GLN A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 33 CD GLN A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 34 OE1 GLN A 4 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 35 NE2 GLN A 4 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 36 N ASN A 5 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 37 CA ASN A 5 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 38 C ASN A 5 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 39 O ASN A 5 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 40 CB ASN A 5 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 41 CG ASN A 5 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 42 OD1 ASN A 5 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 43 ND2 ASN A 5 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 44 N CYS A 6 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 45 CA CYS A 6 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 46 C CYS A 6 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 47 O CYS A 6 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 48 CB CYS A 6 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 49 SG CYS A 6 0.000 0.000 0.000 1.00 0.00 S 79: ATOM 50 N PRO A 7 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 51 CA PRO A 7 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 52 C PRO A 7 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 53 O PRO A 7 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 54 CB PRO A 7 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 55 CG PRO A 7 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 56 CD PRO A 7 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 57 N LEU A 8 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 58 CA LEU A 8 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 59 C LEU A 8 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 60 O LEU A 8 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 61 CB LEU A 8 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 62 CG LEU A 8 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 63 CD1 LEU A 8 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 64 CD2 LEU A 8 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 65 N GLY A 9 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 66 CA GLY A 9 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 67 C GLY A 9 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 68 O GLY A 9 0.000 0.000 0.000 1.00 0.00 O 79: HETATM 69 N NH2 A 10 0.000 0.000 0.000 1.00 0.00 N 79: CONECT 1 2 79: CONECT 2 3 5 79: CONECT 3 4 4 7 79: CONECT 5 6 79: CONECT 6 49 79: CONECT 7 8 79: CONECT 8 9 11 79: CONECT 9 10 10 19 79: CONECT 11 12 79: CONECT 12 13 13 14 79: CONECT 13 15 79: CONECT 14 16 16 79: CONECT 15 17 17 79: CONECT 16 17 79: CONECT 17 18 79: CONECT 19 20 79: CONECT 20 21 23 79: CONECT 21 22 22 27 79: CONECT 23 24 25 79: CONECT 25 26 79: CONECT 27 28 79: CONECT 28 29 31 79: CONECT 29 30 30 36 79: CONECT 31 32 79: CONECT 32 33 79: CONECT 33 34 34 35 79: CONECT 36 37 79: CONECT 37 38 40 79: CONECT 38 39 39 44 79: CONECT 40 41 79: CONECT 41 42 42 43 79: CONECT 44 45 79: CONECT 45 46 48 79: CONECT 46 47 47 50 79: CONECT 48 49 79: CONECT 50 51 56 79: CONECT 51 52 54 79: CONECT 52 53 53 57 79: CONECT 54 55 79: CONECT 55 56 79: CONECT 57 58 79: CONECT 58 59 61 79: CONECT 59 60 60 65 79: CONECT 61 62 79: CONECT 62 63 64 79: CONECT 65 66 79: CONECT 66 67 79: CONECT 67 68 68 69 79: END 79: 79: Sequence: LfPVXLfPVX 79: HELM: PEPTIDE1{L.[dF].P.V.[Orn].L.[dF].P.V.[Orn]}$PEPTIDE1,PEPTIDE1,10:R2-1:R1$$$ 79: 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 79: PDB: 79: ATOM 1 N LEU A 1 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 2 CA LEU A 1 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 3 C LEU A 1 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 4 O LEU A 1 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 5 CB LEU A 1 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 6 CG LEU A 1 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 7 CD1 LEU A 1 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 8 CD2 LEU A 1 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 9 N DPN A 2 0.000 0.000 0.000 1.00 0.00 N 79: HETATM 10 CA DPN A 2 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 11 C DPN A 2 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 12 O DPN A 2 0.000 0.000 0.000 1.00 0.00 O 79: HETATM 13 CB DPN A 2 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 14 CG DPN A 2 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 15 CD1 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 16 CD2 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 17 CE1 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 18 CE2 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 19 CZ DPN A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 20 N PRO A 3 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 21 CA PRO A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 22 C PRO A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 23 O PRO A 3 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 24 CB PRO A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 25 CG PRO A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 26 CD PRO A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 27 N VAL A 4 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 28 CA VAL A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 29 C VAL A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 30 O VAL A 4 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 31 CB VAL A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 32 CG1 VAL A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 33 CG2 VAL A 4 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 34 N ORN A 5 0.000 0.000 0.000 1.00 0.00 N 79: HETATM 35 CA ORN A 5 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 36 C ORN A 5 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 37 O ORN A 5 0.000 0.000 0.000 1.00 0.00 O 79: HETATM 38 CB ORN A 5 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 39 CG ORN A 5 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 40 CD ORN A 5 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 41 NE ORN A 5 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 42 N LEU A 6 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 43 CA LEU A 6 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 44 C LEU A 6 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 45 O LEU A 6 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 46 CB LEU A 6 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 47 CG LEU A 6 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 48 CD1 LEU A 6 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 49 CD2 LEU A 6 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 50 N DPN A 7 0.000 0.000 0.000 1.00 0.00 N 79: HETATM 51 CA DPN A 7 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 52 C DPN A 7 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 53 O DPN A 7 0.000 0.000 0.000 1.00 0.00 O 79: HETATM 54 CB DPN A 7 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 55 CG DPN A 7 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 56 CD1 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 57 CD2 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 58 CE1 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 59 CE2 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 60 CZ DPN A 7 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 61 N PRO A 8 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 62 CA PRO A 8 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 63 C PRO A 8 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 64 O PRO A 8 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 65 CB PRO A 8 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 66 CG PRO A 8 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 67 CD PRO A 8 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 68 N VAL A 9 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 69 CA VAL A 9 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 70 C VAL A 9 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 71 O VAL A 9 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 72 CB VAL A 9 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 73 CG1 VAL A 9 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 74 CG2 VAL A 9 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 75 N ORN A 10 0.000 0.000 0.000 1.00 0.00 N 79: HETATM 76 CA ORN A 10 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 77 C ORN A 10 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 78 O ORN A 10 0.000 0.000 0.000 1.00 0.00 O 79: HETATM 79 CB ORN A 10 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 80 CG ORN A 10 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 81 CD ORN A 10 0.000 0.000 0.000 1.00 0.00 C 79: HETATM 82 NE ORN A 10 0.000 0.000 0.000 1.00 0.00 N 79: CONECT 1 2 77 79: CONECT 2 3 5 79: CONECT 3 4 4 9 79: CONECT 5 6 79: CONECT 6 7 8 79: CONECT 9 10 79: CONECT 10 11 13 79: CONECT 11 12 12 20 79: CONECT 13 14 79: CONECT 14 15 15 16 79: CONECT 15 17 79: CONECT 16 18 18 79: CONECT 17 19 19 79: CONECT 18 19 79: CONECT 20 21 26 79: CONECT 21 22 24 79: CONECT 22 23 23 27 79: CONECT 24 25 79: CONECT 25 26 79: CONECT 27 28 79: CONECT 28 29 31 79: CONECT 29 30 30 34 79: CONECT 31 32 33 79: CONECT 34 35 79: CONECT 35 36 38 79: CONECT 36 37 37 42 79: CONECT 38 39 79: CONECT 39 40 79: CONECT 40 41 79: CONECT 42 43 79: CONECT 43 44 46 79: CONECT 44 45 45 50 79: CONECT 46 47 79: CONECT 47 48 49 79: CONECT 50 51 79: CONECT 51 52 54 79: CONECT 52 53 53 61 79: CONECT 54 55 79: CONECT 55 56 56 57 79: CONECT 56 58 79: CONECT 57 59 59 79: CONECT 58 60 60 79: CONECT 59 60 79: CONECT 61 62 67 79: CONECT 62 63 65 79: CONECT 63 64 64 68 79: CONECT 65 66 79: CONECT 66 67 79: CONECT 68 69 79: CONECT 69 70 72 79: CONECT 70 71 71 75 79: CONECT 72 73 74 79: CONECT 75 76 79: CONECT 76 77 79 79: CONECT 77 78 78 79: CONECT 79 80 79: CONECT 80 81 79: CONECT 81 82 79: END 79: 79: Sequence: GREG 79: HELM: PEPTIDE1{G.R.E.G}$$$$ 79: Smiles: N=C(N)NCCCC(NC(=O)CN)C(=O)NC(CCC(=O)O)C(=O)NCC(=O)O 79: PDB: 79: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 23 OD1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 24 OD2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O 79: CONECT 1 2 79: CONECT 2 3 79: CONECT 3 4 4 5 79: CONECT 5 6 79: CONECT 6 7 9 79: CONECT 7 8 8 16 79: CONECT 9 10 79: CONECT 10 11 79: CONECT 11 12 79: CONECT 12 13 79: CONECT 13 14 14 15 79: CONECT 16 17 79: CONECT 17 18 20 79: CONECT 18 19 19 25 79: CONECT 20 21 79: CONECT 21 22 79: CONECT 22 23 23 24 79: CONECT 25 26 79: CONECT 26 27 79: CONECT 27 28 28 29 79: END 79: 68/235 Test #79: testSequence ........................... Passed 0.06 sec test 80 Start 80: testExtendedStereoParsing 80: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing 80: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 80: Test timeout computed to be: 1500 69: Test 69: 69: BMS-986142_atropBad2.mrv 69: 69: [15:23:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 69/235 Test #80: testExtendedStereoParsing .............. Passed 0.02 sec test 81 Start 81: fileParsersCatchTest 81: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 81: Test timeout computed to be: 1500 69: Test 69: 69: JDQ443_3d.mrv 69: 69: Test 69: 69: JDQ443_atrop1.mrv 69: 69: Test 69: 69: JDQ443_atrop2.mrv 69: 69: Test 69: 69: JDQ443_atrop3.mrv 69: 69: Test 69: 69: JDQ443_atropBad1.mrv 69: 69: [15:23:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 69: Test 69: 69: RP-6306_atrop1.mrv 69: 69: Test 69: 69: RP-6306_atrop2.mrv 69: 69: Test 69: 69: RP-6306_atrop3.mrv 69: 69: Test 69: 69: RP-6306_atrop4.mrv 69: 69: Test 69: 69: RP-6306_atrop5.mrv 69: 69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: Test 69: 69: RP-6306_atropBad1.mrv 69: 69: [15:23:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 69: Test 69: 69: RP-6306_atropBad2.mrv 69: 69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: [15:23:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 81: Randomness seeded to: 3915011631 81: [15:23:08] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 81: [15:23:08] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 81: [15:23:08] Could not infer missing lvIdx on malformed SAP line for SGroup 1 81: [15:23:08] SGroup 1 is invalid and will be ignored 81: [15:23:08] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 81: [15:23:08] Could not infer missing lvIdx on malformed SAP line for SGroup 1 81: [15:23:08] SGroup 1 is invalid and will be ignored 81: [15:23:08] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 81: [15:23:08] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 81: [15:23:08] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 81: [15:23:08] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 81: [15:23:08] Could not infer missing lvIdx on malformed SAP line for SGroup 1 81: [15:23:08] SGroup 1 is invalid and will be ignored 81: [15:23:08] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 81: [15:23:08] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 81: [15:23:08] Could not infer missing lvIdx on malformed SAP line for SGroup 1 81: [15:23:08] SGroup 1 is invalid and will be ignored 81: [15:23:08] SGroup 3 referenced on line 40 not found. 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: no bonds 81: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp 81: Failed Expression: !d_bonds.empty() 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 4# 0x0000FFFFBA89EE88 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# 0x0000AAAABD589D7C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 8# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 9# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 16# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] SGroup 3 referenced on line 40 not found. 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: no bonds 81: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp 81: Failed Expression: !d_bonds.empty() 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 4# 0x0000FFFFBA89EE88 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# 0x0000AAAABD589DFC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 8# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 9# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 16# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] no bonds 81: [15:23:08] SGroup 1 is invalid and will be ignored 81: [15:23:08] SGroup line too short: 'M SBV 1 6' on line 42 81: [15:23:08] SGroup 1 is invalid and will be ignored 81: [15:23:08] SGroup line too short: 'M SBL 2 3 9 10' on line 46 81: [15:23:08] SGroup 2 is invalid and will be ignored 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: bookmark not found 81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp 81: Failed Expression: (lu != d_bondBookmarks.end()) 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# 0x0000FFFFBA89EDF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# 0x0000AAAABD58A7A4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 9# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 15# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 17# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: bookmark not found 81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp 81: Failed Expression: (lu != d_bondBookmarks.end()) 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# 0x0000FFFFBA89EDF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# 0x0000AAAABD58A824 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 9# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 15# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 17# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] bookmark not found 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: bond is not part of the SubstanceGroup 81: Violation occurred on line 200 in file ./Code/GraphMol/SubstanceGroup.cpp 81: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::SubstanceGroup::getBondType(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 4# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# 0x0000FFFFBA89EE88 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# 0x0000AAAABD58A824 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 9# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 15# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 17# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] bond is not part of the SubstanceGroup 81: [15:23:08] SGroup 2 is invalid and will be ignored 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: bookmark not found 81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp 81: Failed Expression: (lu != d_atomBookmarks.end()) 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# 0x0000FFFFBA89EDF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# 0x0000AAAABD58AB14 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 9# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 15# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 17# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: bookmark not found 81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp 81: Failed Expression: (lu != d_atomBookmarks.end()) 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# 0x0000FFFFBA89EDF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# 0x0000AAAABD58AB94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 9# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 15# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 17# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] bookmark not found 81: [15:23:08] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. 81: [15:23:08] SGroup 2 is invalid and will be ignored 81: [15:23:08] WARNING: final character of V3000 array is not ')' 81: [15:23:08] 81: 81: **** 69: Test 69: 69: RP-6306_3d.mrv 69: 69: Test 69: 69: Sotorasib_atrop1.mrv 69: 69: Test 69: 69: Sotorasib_atrop2.mrv 69: 69: Test 69: 69: Sotorasib_atrop3.mrv 69: 69: Test 69: 69: Sotorasib_atrop4.mrv 69: 69: Test 69: 69: Sotorasib_atrop5.mrv 69: 69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: Test 69: 69: Sotorasib_atropBad1.mrv 69: 69: [15:23:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 69: Test 69: 69: Sotorasib_atropBad2.mrv 69: 69: [15:23:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 81: Pre-condition Violation 81: bookmark not found 81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp 81: Failed Expression: (lu != d_bondBookmarks.end()) 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 9# 0x0000AAAABD588798 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] WARNING: final character of V3000 array is not ')' 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: bookmark not found 81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp 81: Failed Expression: (lu != d_bondBookmarks.end()) 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 9# 0x0000AAAABD588814 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] bookmark not found 81: [15:23:08] SGroup 1 is invalid and will be ignored 81: [15:23:08] WARNING: final character of V3000 array is not ')' 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: bookmark not found 81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp 81: Failed Expression: (lu != d_atomBookmarks.end()) 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 9# 0x0000AAAABD588AE8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] WARNING: final character of V3000 array is not ')' 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: bookmark not found 81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp 81: Failed Expression: (lu != d_atomBookmarks.end()) 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 9# 0x0000AAAABD588B64 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] bookmark not found 81: [15:23:08] SGroup 1 is invalid and will be ignored 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: bookmark not found 81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp 81: Failed Expression: (lu != d_bondBookmarks.end()) 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 9# 0x0000AAAABD588E38 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: bookmark not found 81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp 81: Failed Expression: (lu != d_bondBookmarks.end()) 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 9# 0x0000AAAABD588EB4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] bookmark not found 81: [15:23:08] SGroup 2 is invalid and will be ignored 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: bookmark not found 81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp 81: Failed Expression: (lu != d_atomBookmarks.end()) 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 9# 0x0000AAAABD589188 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: bookmark not found 81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp 81: Failed Expression: (lu != d_atomBookmarks.end()) 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 9# 0x0000AAAABD589204 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] bookmark not found 81: [15:23:08] SGroup 2 is invalid and will be ignored 81: [15:23:08] Explicit valence for atom # 2 O, 3, is greater than permitted 81: [15:23:08] Explicit valence for atom # 1 O, 3, is greater than permitted 81: [15:23:08] Explicit valence for atom # 1 C, 5, is greater than permitted 69: Test 69: 69: Sotorasib_3d.mrv 69: 69: Test 69: 69: ZM374979_atrop1.mrv 69: 69: Test 69: 69: ZM374979_atrop2.mrv 69: 69: Test 69: 69: ZM374979_atrop3.mrv 69: 69: Test 69: 69: ZM374979_atropBad1.mrv 69: 69: [15:23:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 81: [15:23:08] sanitize [15:23:08] UNK: [15:23:08] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 81: [15:23:08] skipping block at line 7: 'BEGIN ATOM' 81: ATOM 1 CHLO CHL 0 0.000 0.000 0.000 1.00 0.00 CL 81: END 81: 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: no stream 81: Violation occurred on line 133 in file ./Code/GraphMol/FileParsers/SDMolSupplier.cpp 81: Failed Expression: dp_inStream 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 3# 0x0000AAAABD5BEEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 4# 0x0000AAAABD57B1A4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 5# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 6# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 7# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 8# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 9# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 13# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: no stream 81: Violation occurred on line 187 in file ./Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp 81: Failed Expression: dp_inStream 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::ForwardSDMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 3# 0x0000AAAABD5BEEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 4# 0x0000AAAABD57B314 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 5# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 6# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 7# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 8# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 9# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 13# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: no stream 81: Violation occurred on line 409 in file ./Code/GraphMol/FileParsers/SmilesMolSupplier.cpp 81: Failed Expression: dp_inStream 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::SmilesMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 3# 0x0000AAAABD5BEEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 4# 0x0000AAAABD57B648 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 5# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 6# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 7# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 8# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 9# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 13# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: no stream 81: Violation occurred on line 264 in file ./Code/GraphMol/FileParsers/TDTMolSupplier.cpp 81: Failed Expression: dp_inStream 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::TDTMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 3# 0x0000AAAABD5BEEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 4# 0x0000AAAABD57B8E4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 5# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 6# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 7# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 8# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 9# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 13# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: no stream 81: Violation occurred on line 577 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 81: Failed Expression: dp_sInStream != nullptr 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 3# 0x0000AAAABD5BEEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 4# 0x0000AAAABD57BADC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 5# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 6# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 7# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 8# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 9# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 13# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] Found a SCD/SED line with missing/empty SDT specification at line 21 81: [15:23:08] Found a SCD/SED line with missing/empty SDT specification at line 20 81: [15:23:08] BEGIN SGROUP line not found on line 14 69: Test 69: 69: mrtx1719_3d.mrv 69: 69: Test 69: 69: mrtx1719_atrop1.mrv 69: 69: Test 69: 69: mrtx1719_atrop2.mrv 69: 69: Test 69: 69: mrtx1719_atrop3.mrv 69: 69: Test 69: 69: mrtx1719_atropBad1.mrv 69: 69: [15:23:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 70: ---------------------------------- 70: ---------------------------------- 70: [15:23:08] 70: 70: **** 70: Pre-condition Violation 70: rlabel out of range for MDL files 70: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp 70: Failed Expression: rlabel >= 0 && rlabel < 100 70: ---------- 70: Stacktrace: 70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 70: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 70: 3# 0x0000AAAAC526F2FC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: 4# 0x0000AAAAC52D4BA4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: 5# 0x0000AAAAC5245CB8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: 6# 0x0000FFFFB837229C in /lib/aarch64-linux-gnu/libc.so.6 70: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 70: 8# 0x0000AAAAC5245EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: ---------- 70: **** 70: 70: [15:23:08] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 81: [15:23:08] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. 81: [15:23:08] END SGROUP line not found on line 14 81: [15:23:08] END SGROUP line not found on line 14 81: [15:23:08] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. 81: [15:23:08] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. 81: [15:23:08] 81: 81: **** 81: Range Error 81: idx 81: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp 81: Failed Expression: 99 < 9 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::FileParserUtils::finishMolProcessing(RDKit::RWMol*, bool, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 4# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# 0x0000AAAABD5BEB34 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 7# 0x0000AAAABD580B30 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 8# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 9# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 16# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. 81: [15:23:08] Multiple ATTCHPT values for atom 2 on line 9 81: [15:23:08] Found a SCD/SED line with missing/empty SDT specification at line 12 81: [15:23:08] SMARTS Parse Error: syntax error while parsing: [#6;R 81: [15:23:08] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' 81: [15:23:08] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. 81: [15:23:08] Skipping empty SMARTS value for SMARTSQ. 81: [15:23:08] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. 81: [15:23:08] Found a SCD/SED line with missing/empty SDT specification at line 12 81: [15:23:08] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 81: [15:23:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 81: [15:23:08] WARNING: Skipping property bar because the value includes an illegal blank line 81: [15:23:08] WARNING: Skipping property baz because the value includes an illegal blank line 81: [15:23:08] WARNING: Skipping property bletch 81: nope because the name includes a newline 81: [15:23:08] WARNING: Skipping property bletch 81: nope2 because the name includes a newline 81: [15:23:08] 81: 81: **** 81: Post-condition Violation 81: Element 'QQQ' not found 81: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 81: Failed Expression: anum > -1 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 3# 0x0000FFFFBA887FE4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 4# 0x0000FFFFBA898230 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# 0x0000FFFFBA898E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 9# 0x0000AAAABD554FB4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] 81: 81: **** 81: Post-condition Violation 81: Element 'QQQ' not found 81: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 81: Failed Expression: anum > -1 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 3# 0x0000FFFFBA887FE4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 4# 0x0000FFFFBA898230 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# 0x0000FFFFBA898E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 9# 0x0000AAAABD5548D8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] 81: 81: **** 81: Post-condition Violation 81: Element 'QQQ' not found 81: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 81: Failed Expression: anum > -1 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 3# 0x0000FFFFBA887FE4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 4# 0x0000FFFFBA895BC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# 0x0000FFFFBA896AEC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 9# 0x0000AAAABD554F70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] 81: 81: **** 81: Post-condition Violation 81: Element 'QQQ' not found 81: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 81: Failed Expression: anum > -1 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 3# 0x0000FFFFBA887FE4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 4# 0x0000FFFFBA895BC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# 0x0000FFFFBA896AEC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 9# 0x0000AAAABD554CA8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] atom 3 has a negative isotope value. line: 15 81: [15:23:08] 81: 81: **** 81: Invariant Violation 81: bad prop value 81: Violation occurred on line 155 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 81: Failed Expression: nSwaps < 2 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# 0x0000FFFFBA955C7C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 4# 0x0000AAAABD5BEEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 5# 0x0000AAAABD591EA0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 6# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 7# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 8# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 9# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 12# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 14# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 81: [15:23:08] 81: 81: **** 81: Pre-condition Violation 81: no input stream 81: Violation occurred on line 544 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 81: Failed Expression: dp_sInStream 81: ---------- 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::MaeMolSupplier::init() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 3# RDKit::v2::FileParsers::MaeMolSupplier::reset() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 4# 0x0000AAAABD5921C4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 5# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 6# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 7# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 8# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 9# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 10# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: 11# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 81: 13# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: 76: [15:23:08] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 76: 0.40201265 0.40201265 76: -0.13299436 -0.13299436 76: 1.00000017 1.00000017 76: 0.8762226 0.8762226 76: 0.9973909 0.9973909 76: 1.00000003 1.00000003 76: 0.36613799 0.36613799 76: 2.1107185 2.1107185 76: 0.99999982 0.99999982 76: 2.48696157 2.48696157 76: 1.00479935 1.00479935 76: 0.99999999 0.99999999 76: 3.03311841 3.03311841 76: 2.23739955 2.23739955 76: 1.0000001 1.0000001 76: 3.00772337 3.00772337 76: 0.37399294 0.37399294 76: 2.07713325 2.07713325 76: 3.0077234 3.0077234 76: 0.37399312 0.37399312 76: -0.07713336 -0.07713336 69: Test 69: 69: AlexRxn.mrv 69: 69: Test 69: 69: BadReactionSign.mrv 69: 69: Test 69: 69: bondArray_node.mrv 69: 69: Test 69: 69: marvin03.mrv 69: 69: Test 69: 69: marvin04.mrv 69: 69: Test 69: 69: marvin08.mrv 69: 69: Test 69: 69: marvin09.mrv 69: 69: Test 69: 69: marvin11.mrv 69: 69: Test 69: 69: marvin05.mrv 69: 69: Test 69: 69: EmptyRxn.mrv 69: 69: [15:23:08] initialization failed 76: [15:23:08] bond with order 0 found on line 11. This is not part of the MDL specification. 76: [15:23:08] bond with order 0 found on line 16. This is not part of the MDL specification. 70/235 Test #76: testMolWriter .......................... Passed 0.56 sec test 82 Start 82: testPropertyLists 82: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists 82: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 82: Test timeout computed to be: 1500 81: [15:23:08] ERROR: molecules without atoms cannot be exported to Maestro files. 81: [15:23:08] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 81: [15:23:08] ERROR: the mol cannot be kekulized, and will not be written to the output file. 81: [15:23:08] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. 69: Test 69: 69: RxnNoCoords.mrv 69: 69: Test 69: 69: mrvValenceZero.mrv 69: 69: Test 69: 69: condition_coordinates_mpoint.mrv 69: 69: Test 69: 69: marvin01.mrv 69: 69: Test 69: 69: aspirineSynthesisWithAttributes.mrv 69: 69: Test 69: 69: marvin01.mrv 69: 69: Test 69: 69: NewChiralTest 69: 69: Test 69: 69: NewChiralTest 69: 69: Test 69: 69: NewChiralTestNoChiral 69: 69: Test 69: 69: NewChiralTestNoChiral 69: 69: Test 69: 69: NewChiralTest2 69: 69: Test 69: 69: NewChiralTest2 69: 69: Test 69: 69: NewChiralTest2AllChiral 69: 69: Test 69: 69: NewChiralTest2AllChiral 69: 69: Test 69: 69: Vendor839 69: 69: Test 69: 69: DoubleBondChain 69: 69: Test 69: 69: Na_Mg_Al_OH 69: 69: Test 69: 69: Pb 69: 69: Test 69: 69: O_Mg_Si 69: 69: Test 69: 69: SquiggleBond 69: 69: Test 69: 69: BigMacrocycle 69: 69: Test 69: 69: Smiles1 69: 71/235 Test #69: testMrvToMol ........................... Passed 2.33 sec 81: [15:23:08] WARNING: atom 1 in input Maestro file has atomic number '0', which is reserved for internal use, and not allowed in inputs. The atom will be ignored.[15:23:08] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 81: [15:23:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. test 83 Start 83: XYZFileParserCatchTest 83: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest 83: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 83: Test timeout computed to be: 1500 81: [15:23:08] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 81: [15:23:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 82: Randomness seeded to: 2000095169 82: =============================================================================== 82: All tests passed (95 assertions in 4 test cases) 82: 72/235 Test #82: testPropertyLists ...................... Passed 0.05 sec test 84 Start 84: cdxmlParserCatchTest 84: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest 84: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 84: Test timeout computed to be: 1500 83: Randomness seeded to: 1460572979 83: =============================================================================== 83: All tests passed (100 assertions in 2 test cases) 83: 73/235 Test #83: XYZFileParserCatchTest ................. Passed 0.07 sec test 85 Start 85: molfileStereoCatchTest 85: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest 85: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 85: Test timeout computed to be: 1500 85: Randomness seeded to: 815005210 85: [15:23:08] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 85: [15:23:08] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 85: [15:23:08] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 85: [15:23:08] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 85: =============================================================================== 85: All tests passed (142 assertions in 6 test cases) 85: 74/235 Test #85: molfileStereoCatchTest ................. Passed 0.06 sec test 86 Start 86: connectTheDotsTest 86: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest 86: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 86: Test timeout computed to be: 1500 84: Randomness seeded to: 2434238225 84: [15:23:08] Invalid or missing fragment id from CDXML fragment, assigning new one... 84: [15:23:08] Explicit valence for atom # 3 N, 4, is greater than permitted 84: [15:23:08] CDXMLParser: failed sanitizing skipping fragment 32 84: [15:23:08] Bad bond in CDXML skipping fragment 58... 84: [15:23:08] Invalid or missing fragment id from CDXML fragment, assigning new one... 84: [15:23:08] Bad bond in CDXML skipping fragment 58... 86: Randomness seeded to: 1425021582 86: =============================================================================== 86: All tests passed (8 assertions in 1 test case) 86: 75/235 Test #86: connectTheDotsTest ..................... Passed 0.08 sec test 87 Start 87: v2MolSuppliers 87: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers 87: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 87: Test timeout computed to be: 1500 84: [15:23:08] WARNING: not removing hydrogen atom without neighbors 84: [15:23:08] WARNING: not removing hydrogen atom without neighbors 84: [15:23:08] WARNING: not removing hydrogen atom without neighbors 84: [15:23:08] WARNING: not removing hydrogen atom without neighbors 87: Randomness seeded to: 3820573748 87: =============================================================================== 87: All tests passed (12 assertions in 5 test cases) 87: 76/235 Test #87: v2MolSuppliers ......................... Passed 0.05 sec test 88 Start 88: v2FileParsersCatchTest 88: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest 88: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 88: Test timeout computed to be: 1500 84: [15:23:08] WARNING: not removing hydrogen atom without neighbors 84: [15:23:08] WARNING: not removing hydrogen atom without neighbors 84: [15:23:08] WARNING: not removing hydrogen atom without neighbors 84: [15:23:08] WARNING: not removing hydrogen atom without neighbors 84: [15:23:08] WARNING: not removing hydrogen atom without neighbors 84: [15:23:08] WARNING: not removing hydrogen atom without neighbors 84: [15:23:08] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. 88: Randomness seeded to: 3184513006 88: =============================================================================== 88: All tests passed (6 assertions in 1 test case) 88: 77/235 Test #88: v2FileParsersCatchTest ................. Passed 0.05 sec test 89 Start 89: multithreadedSupplierCatchTest 89: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest 89: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 89: Test timeout computed to be: 1500 84: [15:23:08] Incomplete atom labelling, cannot make bond 84: [15:23:08] Incomplete atom labelling, cannot make bond 84: [15:23:08] Incomplete atom labelling, cannot make bond 70: [15:23:08] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas 70: [15:23:08] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' 84: [15:23:08] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas 84: [15:23:08] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas 84: [15:23:08] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast 84: [15:23:08] Failed to parse XML fragment 5 node: b attribute: Order: 5 84: [15:23:08] Invalid or missing fragment id from CDXML fragment, assigning new one... 84: =============================================================================== 84: All tests passed (263 assertions in 7 test cases) 84: 78/235 Test #84: cdxmlParserCatchTest ................... Passed 0.36 sec test 90 Start 90: testSubstructMatch 90: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct 90: Test timeout computed to be: 1500 90: ----------------- Test 1 90: Done 90: 90: ----------------- Test 2 90: Done 90: 90: ----------------- Test 3 90: Done 90: 90: ----------------- Test 4 90: Done 90: 90: ----------------- Test 5 90: Done 90: 90: ----------------- Test 5 QueryRoot 90: Done 90: 90: ----------------- Test 6 (Issue71 related) 90: Done 90: 90: ----------------- Testing serial numbers on recursive queries 90: Done 90: 90: [15:23:09] ------------------------------------- 90: [15:23:09] Test multithreading 90: reading molecules 70: [15:23:09] Empty atom list: 'M ALS 1 0 F' on line 8. 90: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 90: processing 90: launch :0 90: launch :1 90: launch :2 90: launch :3 70: de_DE.UTF-8 70: [15:23:09] ------------------------------------- 70: [15:23:09] Test multithreading Locale Switching 70: [15:23:09] Test multithreading (Done) 70: [15:23:09] ------------------------------------- 70: *************************************** 70: *************************************** 70: [15:23:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70: [15:23:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70: [15:23:09] bond with order 0 found on line 7. This is not part of the MDL specification. 70: [15:23:09] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) 70: [15:23:09] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) 70: [15:23:09] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 70: generating smiles 70: 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 70: converting back 70: check isomorphism 90: done 90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 90: processing2 90: launch2 :0 90: launch2 :1 90: launch2 :2 90: launch2 :3 90: done 90: preprocessing 3 90: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 90: processing3 90: launch3 :0 90: launch3 :1 90: launch3 :2 90: launch3 :3 89: Randomness seeded to: 3044199220 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 90: done 90: [15:23:09] done 90: [15:23:09] ------------------------------------- 90: [15:23:09] Test GitHub issue 15 90: [15:23:09] done 90: [15:23:09] ------------------------------------- 90: [15:23:09] Test GitHub issue 409 90: [15:23:09] done 90: [15:23:09] ------------------------------------- 90: [15:23:09] Test chiral matching 41: [15:23:09] done: 500000 41: [15:23:09] Done 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 90: [15:23:09] done 90: [15:23:09] ------------------------------------- 90: [15:23:09] Test GitHub issue 688: partially specified chiral substructure queries don't work properly 90: [15:23:09] done 90: [15:23:09] ------------------------------------- 90: [15:23:09] Test dative-bond matching 90: [15:23:09] done 90: [15:23:09] ------------------------------------- 90: [15:23:09] Test cis/trans matching 90: [15:23:09] done 90: [15:23:09] ------------------------------------- 90: [15:23:09] Test cis/trans matching part 2 90: [15:23:09] done 90: [15:23:09] ------------------------------------- 90: [15:23:09] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS 90: [15:23:09] done 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 90: [15:23:09] ------------------------------------- 90: [15:23:09] Testing matching E/Z against Cis/Trans stereo bonds 90: [15:23:09] 90: 90: **** 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 90: Pre-condition Violation 90: matches must not be empty 90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp 90: Failed Expression: !matches.empty() 90: ---------- 90: Stacktrace: 90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 90: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 90: 3# RDKit::getMostSubstitutedCoreMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 90: 4# 0x0000AAAAC5E4AED0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: 5# 0x0000AAAAC5E39AE8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: 6# 0x0000FFFFBA3F229C in /lib/aarch64-linux-gnu/libc.so.6 90: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 90: 8# 0x0000AAAAC5E39CF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: ---------- 90: **** 90: 90: [15:23:09] 90: 90: **** 90: Pre-condition Violation 90: matches must not be empty 90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp 90: Failed Expression: !matches.empty() 90: ---------- 90: Stacktrace: 90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 90: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 90: 3# RDKit::sortMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 90: 4# 0x0000AAAAC5E4B520 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: 5# 0x0000AAAAC5E39AE8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: 6# 0x0000FFFFBA3F229C in /lib/aarch64-linux-gnu/libc.so.6 90: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 90: 8# 0x0000AAAAC5E39CF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: ---------- 90: **** 90: 90: [15:23:09] ------------------------------------- 90: [15:23:09] Test substructure matching with a pathological case for symmetric SSSR 90: [15:23:09] ------------------------------------- 90: [15:23:09] Test isAtomTerminalRGroupOrQueryHydrogen 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 79/235 Test #90: testSubstructMatch ..................... Passed 0.55 sec test 91 Start 91: substructTestCatch 91: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch 91: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct 91: Test timeout computed to be: 1500 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 41: [15:23:09] Testing hanoi with a functor. 41: [15:23:09] Done 41: [15:23:09] Testing basic partition refinement. 41: [15:23:09] Done 41: [15:23:09] Testing partition refinement with neighbors. 41: [15:23:09] Done 41: [15:23:09] testing canonicalization via tie breaking. 41: [15:23:09] Done 41: [15:23:09] testing canonicalization using the wrapper. 41: [15:23:09] Done 41: [15:23:09] testing some specific ordering problems 41: [15:23:09] Finished 41: [15:23:09] testing chiral invariants. 41: [15:23:09] Finished 41: [15:23:09] testing unique ranks in w.r.t. renumbering. 41: [15:23:09] Finished 41: [15:23:09] testing mol fragments. 41: [15:23:09] Finished 41: [15:23:09] testing protein round-tripping. 89: [15:23:10] Explicit valence for atom # 9 N, 6, is greater than permitted 91: Randomness seeded to: 1879666331 91: =============================================================================== 91: All tests passed (242 assertions in 12 test cases) 91: 80/235 Test #91: substructTestCatch ..................... Passed 0.59 sec test 92 Start 92: testGenericGroups 92: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups 92: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups 92: Test timeout computed to be: 1500 12: .................. 12: ---------------------------------------------------------------------- 12: Ran 18 tests in 6.099s 12: 12: OK 89: [15:23:10] Explicit valence for atom # 3 Al, 6, is greater than permitted 89: [15:23:10] Explicit valence for atom # 4 Al, 6, is greater than permitted 81/235 Test #12: pyBV ................................... Passed 7.43 sec test 93 Start 93: testReaction 93: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReaction 93: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 93: Test timeout computed to be: 1500 89: [15:23:10] Explicit valence for atom # 10 Si, 6, is greater than permitted 93: smi: O=C1CNC(=O)CN1 93: 1: O=C1CNC(=O)CN1 93: 2: COOC 93: [15:23:10] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] 93: [15:23:10] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' 93: O=C1CNC(=O)CN1 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 93: [15:23:10] atom 0 in product 0 has multiple charge specifications. 93: mass: 15.0001 93: Oc1ccccn1 93: Oc1ccc[nH]1 41: [15:23:10] Finished 41: [15:23:10] testing stability w.r.t. renumbering. 89: [15:23:10] Explicit valence for atom # 2 O, 4, is greater than permitted 89: [15:23:10] Explicit valence for atom # 3 Al, 6, is greater than permitted 89: [15:23:10] Explicit valence for atom # 3 Be, 4, is greater than permitted 93: [15:23:10] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] 93: [15:23:10] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' 93: [15:23:10] SMARTS Parse Error: syntax error while parsing: ([C:2] 93: [15:23:10] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' 93: [15:23:10] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] 93: [15:23:10] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' 93: [15:23:10] SMARTS Parse Error: syntax error while parsing: [C:2]) 93: [15:23:10] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' 93: [15:23:10] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] 93: [15:23:10] SMILES Parse Error: check for mistakes around position 2: 93: [15:23:10] [Q:1][C:2][C:3](=[O:4])[O:5] 93: [15:23:10] ~^ 93: [15:23:10] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' 93: [15:23:10] reactant 2 has no mapped atoms. 89: [15:23:10] Explicit valence for atom # 27 P, 6, is greater than permitted 41: [15:23:10] Finished 41: [15:23:10] testing smiles round-tripping. 93: [15:23:10] >> Atoms within one molecule have different RXN roles. 93: [15:23:10] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. 93: [15:23:10] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] 93: [15:23:10] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' 93: [15:23:10] SMARTS Parse Error: syntax error while parsing: ([C:2] 93: [15:23:10] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' 93: [15:23:10] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) 93: [15:23:10] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' 93: [15:23:10] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] 93: [15:23:10] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' 93: [15:23:10] reactant 0 has no mapped atoms. 93: [15:23:10] reactant 1 has no mapped atoms. 93: [15:23:10] reactant 3 has no mapped atoms. 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 3 found multiple times. 93: [15:23:10] product atom-mapping number 4 found multiple times. 93: [15:23:10] product atom-mapping number 5 found multiple times. 93: [15:23:10] product atom-mapping number 6 found multiple times. 93: [15:23:10] product atom-mapping number 7 found multiple times. 93: [15:23:10] product atom-mapping number 8 found multiple times. 93: [15:23:10] product atom-mapping number 12 found multiple times. 93: [15:23:10] product atom-mapping number 9 found multiple times. 93: [15:23:10] product atom-mapping number 10 found multiple times. 93: [15:23:10] product atom-mapping number 11 found multiple times. 93: [15:23:10] reactant 0 has no mapped atoms. 93: [15:23:10] reactant 1 has no mapped atoms. 93: [15:23:10] reactant 3 has no mapped atoms. 93: [15:23:10] reactant atom-mapping number 19 found multiple times. 93: [15:23:10] reactant atom-mapping number 25 found multiple times. 93: [15:23:10] reactant atom-mapping number 20 found multiple times. 93: [15:23:10] reactant atom-mapping number 21 found multiple times. 93: [15:23:10] reactant atom-mapping number 22 found multiple times. 93: [15:23:10] reactant atom-mapping number 23 found multiple times. 93: [15:23:10] reactant atom-mapping number 24 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br 93: [15:23:10] product atom-mapping number 5 found multiple times. 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 3 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 4 found multiple times. 93: [15:23:10] product atom-mapping number 5 found multiple times. 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 3 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 4 found multiple times. 93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br 93: [15:23:10] product atom-mapping number 5 found multiple times. 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 3 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 4 found multiple times. 93: [15:23:10] product atom-mapping number 5 found multiple times. 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 3 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 4 found multiple times. 93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 3 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 4 found multiple times. 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 3 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 4 found multiple times. 93: F[C@@](Cl)(Br)O[C@](F)(Cl)Br 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 3 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 4 found multiple times. 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 3 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 4 found multiple times. 93: F[C@](Cl)(Br)O[C@](F)(Cl)Br 93: [15:23:10] product atom-mapping number 4 found multiple times. 93: [15:23:10] product atom-mapping number 3 found multiple times. 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 4 found multiple times. 93: [15:23:10] product atom-mapping number 3 found multiple times. 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 4 found multiple times. 93: [15:23:10] product atom-mapping number 3 found multiple times. 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 4 found multiple times. 93: [15:23:10] product atom-mapping number 3 found multiple times. 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] product atom-mapping number 3 found multiple times. 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 93: [15:23:10] product atom-mapping number 3 found multiple times. 93: [15:23:10] product atom-mapping number 2 found multiple times. 93: [15:23:10] product atom-mapping number 1 found multiple times. 93: [15:23:10] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 93: [15:23:10] product atom-mapping number 6 not found in reactants. 93: [15:23:10] product atom-mapping number 7 not found in reactants. 93: [15:23:10] product atom-mapping number 8 not found in reactants. 93: [15:23:10] product atom-mapping number 7 not found in reactants. 93: [15:23:10] product atom-mapping number 8 not found in reactants. 93: [15:23:10] product atom-mapping number 9 not found in reactants. 93: [15:23:10] product atom-mapping number 10 not found in reactants. 93: [15:23:10] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 6 93: [15:23:10] product atom-mapping number 7 not found in reactants. 93: [15:23:10] product atom-mapping number 8 not found in reactants. 93: [15:23:10] product atom-mapping number 9 not found in reactants. 93: [15:23:10] product atom-mapping number 10 not found in reactants. 93: [15:23:10] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 6 93: smi1 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] 93: smi2 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] 93: [15:23:10] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 41: [15:23:10] Finished 41: [15:23:10] testing github #1567: Non-canonical result from MolFragmentToSmiles() 41: [15:23:10] Finished 70: [15:23:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 70: [15:23:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 70: [15:23:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 70: [15:23:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 70: [15:23:10] deprecated group abbreviation ignored on line 24 82/235 Test #41: hanoiTest .............................. Passed 5.69 sec test 94 Start 94: testReactionFingerprints 94: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints 94: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 94: Test timeout computed to be: 1500 70: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] 70: [15:23:10] 70: 70: **** 70: Post-condition Violation 70: Element 'Mv' not found 70: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 70: Failed Expression: anum > -1 70: ---------- 70: Stacktrace: 70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 70: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 3# 0x0000FFFFB8CA7FE4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 4# 0x0000FFFFB8CB5BC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 5# 0x0000FFFFB8CB6AEC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 9# 0x0000AAAAC525F83C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: 10# 0x0000AAAAC52D4B44 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: 11# 0x0000AAAAC5245D2C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: 12# 0x0000FFFFB837229C in /lib/aarch64-linux-gnu/libc.so.6 70: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 70: 14# 0x0000AAAAC5245EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: ---------- 70: **** 70: 93: [15:23:10] product atom-mapping number 17 not found in reactants. 93: [15:23:10] product atom-mapping number 18 not found in reactants. 93: [15:23:10] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 12 94: [15:23:10] ------------------------------------- 94: [15:23:10] Test Reaction StructuralFingerprint 93: [15:23:10] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) 93: [15:23:10] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) 93: 93: [15:23:10] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels 93: ------------- 93: CCOc1ccccc1 94: [15:23:10] ------------------------------------- 94: [15:23:10] Test Reaction DifferenceFingerprint 83/235 Test #94: testReactionFingerprints ............... Passed 0.14 sec test 95 Start 95: testEnumeration 95: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration 95: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 95: Test timeout computed to be: 1500 70: [15:23:10] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 70: [15:23:10] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 70: ---------------------------------- 70: ---------------------------------- 70: [15:23:10] 70: 70: **** 70: Pre-condition Violation 70: rlabel out of range for MDL files 70: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp 70: Failed Expression: rlabel >= 0 && rlabel < 100 70: ---------- 70: Stacktrace: 70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 70: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 70: 3# 0x0000AAAAC526F2FC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: 4# 0x0000AAAAC52D4BA4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: 5# 0x0000AAAAC5245D2C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: 6# 0x0000FFFFB837229C in /lib/aarch64-linux-gnu/libc.so.6 70: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 70: 8# 0x0000AAAAC5245EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: ---------- 70: **** 70: 92: Randomness seeded to: 2909242045 92: =============================================================================== 92: All tests passed (11480 assertions in 38 test cases) 92: 84/235 Test #92: testGenericGroups ...................... Passed 0.65 sec test 96 Start 96: rxnTestCatch 96: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch 96: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 96: Test timeout computed to be: 1500 70: [15:23:10] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 95: 30000000 30000000 96: Randomness seeded to: 1199136542 96: [15:23:10] atom 0 in product 0 has multiple charge specifications. 96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 34 96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 36 96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 38 96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 40 96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 42 96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 87 96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 89 96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 91 96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 93 96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 95 96: [15:23:10] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 96: [15:23:10] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 96: [15:23:10] SMARTS Parse Error: unclosed ring for input: 'CC1' 96: [15:23:10] SMILES Parse Error: unclosed ring for input: 'CC1' 96: [15:23:10] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 96: [15:23:10] product atom-mapping number 2 not found in reactants. 96: [15:23:10] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 96: [15:23:10] product atom-mapping number 2 not found in reactants. 96: [15:23:10] CX Extensions: Substance group hierarchy is not always preserved. 96: [15:23:10] CX Extensions: Substance group hierarchy is not always preserved. 93: [15:23:10] reactant 0 has no mapped atoms. 93: [15:23:10] product 0 has no mapped atoms. 93: [15:23:10] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. 96: [15:23:10] reactant 0 has no mapped atoms. 96: [15:23:10] product 0 has no mapped atoms. 96: [15:23:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 96: [15:23:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 96: [15:23:10] Explicit valence for atom # 1 O, 5, is greater than permitted 85/235 Test #93: testReaction ........................... Passed 0.65 sec test 97 Start 97: pyChemReactions 97: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" 97: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 97: Test timeout computed to be: 1500 96: =============================================================================== 96: All tests passed (722 assertions in 30 test cases) 96: 86/235 Test #96: rxnTestCatch ........................... Passed 0.11 sec test 98 Start 98: pyChemReactionEnumerations 98: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" 98: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 98: Test timeout computed to be: 1500 89: [15:23:10] Explicit valence for atom # 9 N, 6, is greater than permitted 70: [15:23:11] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas 70: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' 29: All 191 tests passed 70: [15:23:11] Empty atom list: 'M ALS 1 0 F' on line 8. 87/235 Test #70: fileParsersTest1 ....................... Passed 4.77 sec test 99 Start 99: pyChemReactionSanitize 99: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" 99: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 99: Test timeout computed to be: 1500 89: [15:23:11] Explicit valence for atom # 3 Al, 6, is greater than permitted 89: [15:23:11] Explicit valence for atom # 4 Al, 6, is greater than permitted 89: [15:23:11] Explicit valence for atom # 10 Si, 6, is greater than permitted 29: 29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... 89: [15:23:11] Explicit valence for atom # 2 O, 4, is greater than permitted 98: [15:23:11] == testCartesianProduct 99: .[15:23:11] reactant 0 has no mapped atoms. 99: [15:23:11] product 0 has no mapped atoms. 99: [15:23:11] reactant 0 has no mapped atoms. 99: [15:23:11] product 0 has no mapped atoms. 98: .[15:23:11] == testEnumerateLibrary 97: ...[15:23:11] 97: 97: **** 98: /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> 98: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) 98: ResourceWarning: Enable tracemalloc to get the object allocation traceback 89: [15:23:11] Explicit valence for atom # 3 Al, 6, is greater than permitted 89: [15:23:11] Explicit valence for atom # 3 Be, 4, is greater than permitted 99: .[15:23:11] reactant 0 has no mapped atoms. 99: [15:23:11] reactant 1 has no mapped atoms. 99: [15:23:11] product 0 has no mapped atoms. 99: [15:23:11] reactant 0 has no mapped atoms. 99: [15:23:11] reactant 1 has no mapped atoms. 99: [15:23:11] product 0 has no mapped atoms. 99: [15:23:11] reactant 0 has no mapped atoms. 99: [15:23:11] reactant 1 has no mapped atoms. 99: [15:23:11] product 0 has no mapped atoms. 99: [15:23:11] reactant 0 has no mapped atoms. 99: [15:23:11] reactant 1 has no mapped atoms. 99: [15:23:11] product 0 has no mapped atoms. 99: [15:23:11] reactant 0 has no mapped atoms. 99: [15:23:11] reactant 1 has no mapped atoms. 99: [15:23:11] product 0 has no mapped atoms. 99: [15:23:11] reactant 0 has no mapped atoms. 99: [15:23:11] reactant 1 has no mapped atoms. 99: [15:23:11] product 0 has no mapped atoms. 99: [15:23:11] reactant 0 has no mapped atoms. 99: [15:23:11] reactant 1 has no mapped atoms. 99: [15:23:11] product 0 has no mapped atoms. 99: [15:23:11] reactant 0 has no mapped atoms. 99: [15:23:11] reactant 1 has no mapped atoms. 99: [15:23:11] product 0 has no mapped atoms. 99: [15:23:11] reactant 0 has no mapped atoms. 99: [15:23:11] reactant 1 has no mapped atoms. 99: [15:23:11] product 0 has no mapped atoms. 99: [15:23:11] reactant 0 has no mapped atoms. 99: [15:23:11] reactant 1 has no mapped atoms. 99: [15:23:11] product 0 has no mapped atoms. 99: [15:23:11] reactant 0 has no mapped atoms. 99: [15:23:11] reactant 1 has no mapped atoms. 99: [15:23:11] product 0 has no mapped atoms. 99: [15:23:11] reactant 0 has no mapped atoms. 99: [15:23:11] reactant 1 has no mapped atoms. 99: [15:23:11] product 0 has no mapped atoms. 99: [15:23:11] reactant 0 has no mapped atoms. 99: [15:23:11] reactant 1 has no mapped atoms. 99: [15:23:11] product 0 has no mapped atoms. 99: [15:23:11] reactant 0 has no mapped atoms. 99: [15:23:11] reactant 1 has no mapped atoms. 99: [15:23:11] product 0 has no mapped atoms. 99: () 99: ******************************************** 99: $RXN 99: 99: RDKit 99: 99: 2 1 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 1 0 0 0 0 0 0999 V2000 99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 1 2 1 0 99: M RGP 1 2 1 99: V 1 halogen.bromine.aromatic 99: V 2 [*:1] 99: M STY 1 1 DAT 99: M SAL 1 1 1 99: M SED 1 [#35&$([Br&$(Br-&!@c)])] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 4 3 0 1 0 0 0 0 0 0999 V2000 99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 2 3 1 0 99: 1 2 1 0 99: 2 4 1 0 99: M RGP 1 1 2 99: V 1 [*:2] 99: V 2 boronicacid 99: M STY 1 1 DAT 99: M SAL 1 1 2 99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 0 0 0 0 0 0 0999 V2000 99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 99: 1 2 1 0 99: M RGP 2 1 1 2 2 99: V 1 [*:1] 99: V 2 [*:2] 99: M END 99: 99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 99: $RXN 99: 99: RDKit 99: 99: 2 1 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 1 0 0 0 0 0 0999 V2000 99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 1 2 1 0 99: M RGP 1 2 1 99: V 1 halogen.bromine.aromatic 99: V 2 [*:1] 99: M STY 1 1 DAT 99: M SAL 1 1 1 99: M SED 1 [#35&$([Br&$(Br-&!@c)])] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 4 3 0 1 0 0 0 0 0 0999 V2000 99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 2 3 1 0 99: 1 2 1 0 99: 2 4 1 0 99: M RGP 1 1 2 99: V 1 [*:2] 99: V 2 boronicacid 99: M STY 1 1 DAT 99: M SAL 1 1 2 99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 0 0 0 0 0 0 0999 V2000 99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 99: 1 2 1 0 99: M RGP 2 1 1 2 2 99: V 1 [*:1] 99: V 2 [*:2] 99: M END 99: 99: ******************************************** 99: $RXN 99: 99: RDKit 99: 99: 2 1 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 1 0 0 0 0 0 0999 V2000 99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 99: 1 2 1 0 99: M RGP 1 2 1 99: V 1 halogen.bromine.aromatic 99: V 2 * 99: M STY 1 1 DAT 99: M SAL 1 1 1 99: M SED 1 [#35&$([Br&$(Br-&!@c)])] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 4 3 0 1 0 0 0 0 0 0999 V2000 99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 2 3 1 0 99: 1 2 1 0 99: 2 4 1 0 99: M RGP 1 1 2 99: V 1 * 99: V 2 boronicacid 99: M STY 1 1 DAT 99: M SAL 1 1 2 99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 0 0 0 0 0 0 0999 V2000 99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 99: 1 2 1 0 99: M RGP 2 1 1 2 2 99: V 1 * 99: V 2 * 99: M END 99: 99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 99: $RXN 99: 99: RDKit 99: 99: 2 1 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 1 0 0 0 0 0 0999 V2000 99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 1 2 1 0 99: M RGP 1 2 1 99: V 1 halogen.bromine.aromatic 99: V 2 [*:1] 99: M STY 1 1 DAT 99: M SAL 1 1 1 99: M SED 1 [#35&$([Br&$(Br-&!@c)])] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 4 3 0 1 0 0 0 0 0 0999 V2000 99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 2 3 1 0 99: 1 2 1 0 99: 2 4 1 0 99: M RGP 1 1 2 99: V 1 [*:2] 99: V 2 boronicacid 99: M STY 1 1 DAT 99: M SAL 1 1 2 99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 0 0 0 0 0 0 0999 V2000 99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 99: 1 2 1 0 99: M RGP 2 1 1 2 2 99: V 1 [*:1] 99: V 2 [*:2] 99: M END 99: 99: ******************************************** 99: $RXN 99: 99: RDKit 99: 99: 2 1 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 1 0 0 0 0 0 0999 V2000 99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 99: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 99: 1 2 1 0 99: M ISO 1 2 1 99: V 1 halogen.bromine.aromatic 99: M STY 1 1 DAT 99: M SAL 1 1 1 99: M SED 1 [#35&$([Br&$(Br-&!@c)])] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 4 3 0 1 0 0 0 0 0 0999 V2000 99: 3.4375 -7.7917 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 2 3 1 0 99: 1 2 1 0 99: 2 4 1 0 99: M ISO 1 1 2 99: V 2 boronicacid 99: M STY 1 1 DAT 99: M SAL 1 1 2 99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 0 0 0 0 0 0 0999 V2000 99: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 99: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 99: 1 2 1 0 99: M ISO 2 1 1 2 2 99: M END 99: 99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 99: $RXN 99: 99: RDKit 99: 99: 2 1 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 1 0 0 0 0 0 0999 V2000 99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 1 2 1 0 99: M RGP 1 2 1 99: V 1 halogen.bromine.aromatic 99: V 2 [*:1] 99: M STY 1 1 DAT 99: M SAL 1 1 1 99: M SED 1 [#35&$([Br&$(Br-&!@c)])] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 4 3 0 1 0 0 0 0 0 0999 V2000 99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 2 3 1 0 99: 1 2 1 0 99: 2 4 1 0 99: M RGP 1 1 2 99: V 1 [*:2] 99: V 2 boronicacid 99: M STY 1 1 DAT 99: M SAL 1 1 2 99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 0 0 0 0 0 0 0999 V2000 99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 99: 1 2 1 0 99: M RGP 2 1 1 2 2 99: V 1 [*:1] 99: V 2 [*:2] 99: M END 99: 99: ******************************************** 99: $RXN 99: 99: RDKit 99: 99: 2 1 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 1 0 0 0 0 0 0999 V2000 99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 99: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 99: 1 2 1 0 99: M ISO 1 2 1 99: V 1 halogen.bromine.aromatic 99: M STY 1 1 DAT 99: M SAL 1 1 1 99: M SED 1 [#35&$([Br&$(Br-&!@c)])] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 4 3 0 1 0 0 0 0 0 0999 V2000 99: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 2 3 1 0 99: 1 2 1 0 99: 2 4 1 0 99: M ISO 1 1 3 99: V 2 boronicacid 99: M STY 1 1 DAT 99: M SAL 1 1 2 99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 0 0 0 0 0 0 0999 V2000 99: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 99: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 99: 1 2 1 0 99: M ISO 2 1 1 2 2 99: M END 99: [15:23:11] reactant 0 has no mapped atoms. 99: [15:23:11] reactant 1 has no mapped atoms. 99: [15:23:11] product 0 has no mapped atoms. 99: [15:23:11] Could not find RLabel mapping for atom: 0 in template: 1 99: [15:23:11] reactant 1 has no mapped atoms. 99: [15:23:11] reactant 1 has no mapped atoms. 99: [15:23:11] reactant 1 has no mapped atoms. 99: .. 99: ---------------------------------------------------------------------- 99: Ran 4 tests in 0.060s 99: 99: OK 99: 99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 99: $RXN 99: 99: RDKit 99: 99: 2 1 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 1 0 0 0 0 0 0999 V2000 99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 1 2 1 0 99: M RGP 1 2 1 99: V 1 halogen.bromine.aromatic 99: V 2 [*:1] 99: M STY 1 1 DAT 99: M SAL 1 1 1 99: M SED 1 [#35&$([Br&$(Br-&!@c)])] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 4 3 0 1 0 0 0 0 0 0999 V2000 99: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 99: 2 3 1 0 99: 1 2 1 0 99: 2 4 1 0 99: M ISO 1 1 3 99: V 2 boronicacid 99: M STY 1 1 DAT 99: M SAL 1 1 2 99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 99: M END 99: $MOL 99: 99: RDKit 2D 99: 99: 2 1 0 0 0 0 0 0 0 0999 V2000 99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 99: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 99: 1 2 1 0 99: M ISO 1 2 2 99: M RGP 1 1 1 99: V 1 [*:1] 99: M END 99: 99: $RXN Failed 97: Pre-condition Violation 97: getNumImplicitHs() called without preceding call to calcImplicitValence() 97: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp 97: Failed Expression: d_implicitValence > -1 97: ---------- 97: Stacktrace: 97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 97: 25# 0x0000FFFF86F02680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so 97: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 97: 36# 0x0000FFFF8550B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 97: 37# 0x0000FFFF8550B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 97: 38# 0x0000FFFF8550B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 97: 39# 0x0000FFFF8550B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 97: 40# 0x0000FFFF8550B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 97: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 97: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 97: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 97: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 97: 46# 0x0000FFFF86EFF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 97: 47# _PyObject_MakeTpCall in /usr/bin/python3 97: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 49# 0x00000000005335D0 in /usr/bin/python3 97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 51# 0x00000000004AC3B4 in /usr/bin/python3 97: 52# 0x0000000000665934 in /usr/bin/python3 97: 53# _PyObject_MakeTpCall in /usr/bin/python3 97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 55# 0x00000000005335D0 in /usr/bin/python3 97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 57# 0x00000000004AC3B4 in /usr/bin/python3 97: 58# 0x0000000000665934 in /usr/bin/python3 97: 59# _PyObject_MakeTpCall in /usr/bin/python3 97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 61# 0x00000000005335D0 in /usr/bin/python3 97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 63# 0x00000000004AC3B4 in /usr/bin/python3 97: 64# 0x0000000000665934 in /usr/bin/python3 97: 65# _PyObject_MakeTpCall in /usr/bin/python3 97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 67# 0x00000000005051B0 in /usr/bin/python3 97: 68# _PyObject_MakeTpCall in /usr/bin/python3 97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 70# PyEval_EvalCode in /usr/bin/python3 97: 71# 0x00000000005FFD24 in /usr/bin/python3 97: 72# 0x00000000005F9904 in /usr/bin/python3 97: 73# 0x0000000000627ED4 in /usr/bin/python3 97: 74# 0x0000000000627274 in /usr/bin/python3 97: 75# 0x0000000000627010 in /usr/bin/python3 97: 76# Py_RunMain in /usr/bin/python3 97: 77# Py_BytesMain in /usr/bin/python3 97: 78# 0x0000FFFF87A3229C in /lib/aarch64-linux-gnu/libc.so.6 97: 79# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 97: 80# _start in /usr/bin/python3 97: ---------- 97: **** 97: 97: [15:23:11] 97: 97: **** 97: Pre-condition Violation 97: getNumImplicitHs() called without preceding call to calcImplicitValence() 97: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp 97: Failed Expression: d_implicitValence > -1 97: ---------- 97: Stacktrace: 97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 97: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 97: 25# 0x0000FFFF86F02680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so 97: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 97: 36# 0x0000FFFF8550B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 97: 37# 0x0000FFFF8550B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 97: 38# 0x0000FFFF8550B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 97: 39# 0x0000FFFF8550B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 97: 40# 0x0000FFFF8550B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 97: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 97: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 97: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 97: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 97: 46# 0x0000FFFF86EFF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 97: 47# _PyObject_MakeTpCall in /usr/bin/python3 97: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 49# 0x00000000005335D0 in /usr/bin/python3 97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 51# 0x00000000004AC3B4 in /usr/bin/python3 97: 52# 0x0000000000665934 in /usr/bin/python3 97: 53# _PyObject_MakeTpCall in /usr/bin/python3 97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 55# 0x00000000005335D0 in /usr/bin/python3 97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 57# 0x00000000004AC3B4 in /usr/bin/python3 97: 58# 0x0000000000665934 in /usr/bin/python3 97: 59# _PyObject_MakeTpCall in /usr/bin/python3 97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 61# 0x00000000005335D0 in /usr/bin/python3 97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 63# 0x00000000004AC3B4 in /usr/bin/python3 97: 64# 0x0000000000665934 in /usr/bin/python3 97: 65# _PyObject_MakeTpCall in /usr/bin/python3 97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 67# 0x00000000005051B0 in /usr/bin/python3 97: 68# _PyObject_MakeTpCall in /usr/bin/python3 97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 70# PyEval_EvalCode in /usr/bin/python3 97: 71# 0x00000000005FFD24 in /usr/bin/python3 97: 72# 0x00000000005F9904 in /usr/bin/python3 97: 73# 0x0000000000627ED4 in /usr/bin/python3 97: 74# 0x0000000000627274 in /usr/bin/python3 97: 75# 0x0000000000627010 in /usr/bin/python3 97: 76# Py_RunMain in /usr/bin/python3 97: 77# Py_BytesMain in /usr/bin/python3 97: 78# 0x0000FFFF87A3229C in /lib/aarch64-linux-gnu/libc.so.6 97: 79# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 97: 80# _start in /usr/bin/python3 97: ---------- 97: **** 97: 88/235 Test #43: resMolSupplierTest ..................... Passed 7.04 sec test 100 Start 100: testChemTransforms 100: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms 100: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms 100: Test timeout computed to be: 1500 97: .........[15:23:11] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 97: [15:23:11] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 97: [15:23:11] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 97: [15:23:11] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 97: .[15:23:11] product atom-mapping number 1 found multiple times. 97: [15:23:11] product atom-mapping number 1 found multiple times. 97: ................[15:23:11] mapped atoms in the reactants were not mapped in the products. 97: unmapped numbers are: 3 97: [15:23:11] mapped atoms in the reactants were not mapped in the products. 97: unmapped numbers are: 3 97: .:488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. 97: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. 97: [15:23:11] mapped atoms in the reactants were not mapped in the products. 97: unmapped numbers are: 3 97: ..[15:23:11] reactant 2 has no mapped atoms. 97: [15:23:11] reactant 2 has no mapped atoms. 97: [15:23:11] product 1 has no mapped atoms. 97: ........[15:23:11] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q 97: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' 97: [15:23:11] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q 97: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' 97: .[15:23:11] reactant atom-mapping number 1 found multiple times. 97: [15:23:11] product atom-mapping number 2 not found in reactants. 97: [15:23:11] mapped atoms in the reactants were not mapped in the products. 97: unmapped numbers are: 4 97: [15:23:11] product atom-mapping number 5 not found in reactants. 98: ..[15:23:11] == testRGroupState 100: 1 smi: CC 100: 1 smi: CC 100: 2 smi: CCO[C@H](N)P 100: 2 smi: CC 89: [15:23:11] Explicit valence for atom # 27 P, 6, is greater than permitted 100: replaceSub smi1:CCP(CC)[C@@H](N)O 100: replaceSub smi1:CCNCC 98: .[15:23:11] == testRandomEnumerateAllBBsLibrary 98: ** [1, 1] 98: ** [0, 2] 98: ** [1, 0] 100: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O 100: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O 97: ........./build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> 97: png = open(fname, 'rb').read() 97: ResourceWarning: Enable tracemalloc to get the object allocation traceback 97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 34 97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 36 97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 38 97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 40 97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 42 97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 87 97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 89 97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 91 97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 93 97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 95 98: .[15:23:11] == testRandomEnumerateLibrary 98: .[15:23:11] == testRandomSample 98: .[15:23:11] == testRandomSampleAllBBs 100: [15:23:11] SMARTS Parse Error: syntax error while parsing: bar 100: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' 97: ..[15:23:11] SMARTS Parse Error: syntax error while parsing: boromicacid 97: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' 97: [15:23:11] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide 97: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' 97: [15:23:11] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride 97: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' 97: [15:23:11] reaction has no reactants 97: [15:23:11] reaction has no products 97: [15:23:11] initialization failed 97: [15:23:11] reaction has no reactants 97: [15:23:11] reaction has no products 89/235 Test #99: pyChemReactionSanitize ................. Passed 0.86 sec test 101 Start 101: chemTransformsTestCatch 101: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms 101: Test timeout computed to be: 1500 98: .[15:23:11] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 98: [15:23:11] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 98: .[15:23:11] == testRemoveBadMatches 98: .[15:23:11] == testTimings 97: .[15:23:11] SMARTS Parse Error: syntax error while parsing: boromicacid 97: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' 97: [15:23:11] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide 97: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' 97: [15:23:11] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride 97: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' 97: [15:23:11] reaction has no reactants 97: [15:23:11] reaction has no products 97: [15:23:11] initialization failed 97: [15:23:11] reaction has no reactants 97: [15:23:11] reaction has no products 97: . 97: ---------------------------------------------------------------------- 97: Ran 54 tests in 0.231s 97: 97: OK 97: ******************************************** 97: /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/testData/AmideBond.rxn 97: 90/235 Test #100: testChemTransforms ..................... Passed 0.16 sec test 102 Start 102: tautomerQueryTestCatch 102: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch 102: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery 102: Test timeout computed to be: 1500 89: =============================================================================== 89: All tests passed (21562 assertions in 3 test cases) 89: 91/235 Test #89: multithreadedSupplierCatchTest ......... Passed 3.14 sec test 103 Start 103: pyTautomerQuery 103: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" 103: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap 103: Test timeout computed to be: 1500 101: Randomness seeded to: 3917734909 101: [15:23:12] Incomplete atom labelling, cannot make bond 101: [15:23:12] 101: 101: **** 101: Invariant Violation 101: molzip: bond info already exists for end atom with label:1 101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 101: Failed Expression: !bond.b 101: ---------- 101: Stacktrace: 101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 4# 0x0000AAAAB8F06F60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 5# 0x0000AAAAB8F550AC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 6# 0x0000AAAAB8F55A60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 7# 0x0000AAAAB8F55E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 8# 0x0000AAAAB8F2A418 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 9# 0x0000AAAAB8F2A964 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 10# 0x0000AAAAB8EFC4D0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 11# 0x0000FFFFAB2B229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 101: 13# 0x0000AAAAB8EFC5B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: 101: [15:23:12] Incomplete atom labelling, cannot make bond 101: [15:23:12] 101: 101: **** 101: Invariant Violation 101: molzip: bond info already exists for end atom with label:1 101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 101: Failed Expression: !bond.b 101: ---------- 101: Stacktrace: 101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 4# 0x0000AAAAB8F06F60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 5# 0x0000AAAAB8F550AC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 6# 0x0000AAAAB8F55A60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 7# 0x0000AAAAB8F55E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 8# 0x0000AAAAB8F2A418 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 9# 0x0000AAAAB8F2A964 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 10# 0x0000AAAAB8EFC4D0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 11# 0x0000FFFFAB2B229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 101: 13# 0x0000AAAAB8EFC5B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: 101: [15:23:12] Incomplete atom labelling, cannot make bond 101: [15:23:12] 101: 101: **** 101: Invariant Violation 101: molzip: bond info already exists for end atom with label:1 101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 101: Failed Expression: !bond.b 101: ---------- 101: Stacktrace: 101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 4# 0x0000AAAAB8F06F60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 5# 0x0000AAAAB8F550AC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 6# 0x0000AAAAB8F55A60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 7# 0x0000AAAAB8F55E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 8# 0x0000AAAAB8F2A418 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 9# 0x0000AAAAB8F2A964 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 10# 0x0000AAAAB8EFC4D0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 11# 0x0000FFFFAB2B229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 101: 13# 0x0000AAAAB8EFC5B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: 92/235 Test #97: pyChemReactions ........................ Passed 1.27 sec test 104 Start 104: testSubgraphs1 104: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 104: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs 104: Test timeout computed to be: 1500 101: [15:23:12] Incomplete atom labelling, cannot make bond 101: [15:23:12] Incomplete atom labelling, cannot make bond 101: [15:23:12] Incomplete atom labelling, cannot make bond 101: [15:23:12] 101: 101: **** 101: Invariant Violation 101: molzip: bond info already exists for end atom with label:1 101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 101: Failed Expression: !bond.b 101: ---------- 101: Stacktrace: 101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 4# 0x0000AAAAB8F06F60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 5# 0x0000AAAAB8F550AC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 6# 0x0000AAAAB8F55A60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 7# 0x0000AAAAB8F55E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 8# 0x0000AAAAB8F2A418 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 9# 0x0000AAAAB8F2A964 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 10# 0x0000AAAAB8EFC4D0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 11# 0x0000FFFFAB2B229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 101: 13# 0x0000AAAAB8EFC5B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: 101: [15:23:12] Incomplete atom labelling, cannot make bond 101: [15:23:12] 101: 101: **** 101: Invariant Violation 101: molzip: bond info already exists for end atom with label:1 101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 101: Failed Expression: !bond.b 101: ---------- 101: Stacktrace: 101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 4# 0x0000AAAAB8F06F60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 5# 0x0000AAAAB8F550AC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 6# 0x0000AAAAB8F55A60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 7# 0x0000AAAAB8F55E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 8# 0x0000AAAAB8F2A418 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 9# 0x0000AAAAB8F2A964 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 10# 0x0000AAAAB8EFC4D0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 11# 0x0000FFFFAB2B229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 101: 13# 0x0000AAAAB8EFC5B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: 104: ----------------------- 104: Subgraph retrieval 101: [15:23:12] 101: 101: **** 101: Invariant Violation 101: molzip: zipped Bond already exists, perhaps labels are duplicated 101: Violation occurred on line 735 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 101: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) 101: ---------- 101: Stacktrace: 101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 5# 0x0000AAAAB8EFD298 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 6# 0x0000AAAAB8F550AC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 7# 0x0000AAAAB8F55A60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 8# 0x0000AAAAB8F55E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 9# 0x0000AAAAB8F2A418 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 10# 0x0000AAAAB8F2A964 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 11# 0x0000AAAAB8EFC4D0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: 12# 0x0000FFFFAB2B229C in /lib/aarch64-linux-gnu/libc.so.6 101: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 101: 14# 0x0000AAAAB8EFC5B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: 101: =============================================================================== 101: All tests passed (674 assertions in 9 test cases) 101: 93/235 Test #101: chemTransformsTestCatch ................ Passed 0.22 sec test 105 Start 105: testSubgraphs2 105: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 105: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs 105: Test timeout computed to be: 1500 104: Finished 104: ----------------------- 104: testSubgraphs2a 104: Finished 104: ----------------------- 104: testSubgraphs2 105: ----------------------- 105: Test1: pathToSubmol 105: Finished 104: Finished 104: ----------------------- 104: Path retrieval 105: ----------------------- 105: Test2: Atom Environments 105: Finished 105: ----------------------- 105: Test 3: Atom Environments (Extension) 104: Finished 104: ----------------------- 104: Path retrieval2 104: Finished 104: ----------------------- 104: Unique Subgraph retrieval 104: Finished 104: ----------------------- 104: testUniqueSubgraphs2 105: Finished 105: ----------------------- 105: Testing github Issue103: stereochemistry and pathToSubmol 105: Finished 105: ----------------------- 105: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) 105: Finished 94/235 Test #105: testSubgraphs2 ......................... Passed 0.10 sec test 106 Start 106: subgraphsCatch 106: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch 106: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs 106: Test timeout computed to be: 1500 102: Randomness seeded to: 2267052945 102: =============================================================================== 102: All tests passed (93 assertions in 13 test cases) 102: 95/235 Test #102: tautomerQueryTestCatch ................. Passed 0.35 sec test 107 Start 107: filterCatalogTest 107: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest 107: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog 107: Test timeout computed to be: 1500 103: ..... 103: ---------------------------------------------------------------------- 103: Ran 5 tests in 0.053s 103: 103: OK 107: Warning: molecule failed filter 107: Warning: molecule failed filter: reason hzone_phenol_A(479) 107: v = { 107: 0,23}, 107: 1,22}, 107: 2,20}, 107: 3,19}, 107: 4,25}, 107: 5,24}, 107: 6,18}, 107: 7,17}, 107: 8,16}, 107: 9,21}, 107: } 107: match = { 107: 0,23}, 107: 1,22}, 107: 2,20}, 107: 3,19}, 107: 4,25}, 107: 5,24}, 107: 6,18}, 107: 7,17}, 107: 8,16}, 107: 9,21}, 107: } 107: Warning: molecule failed filter 107: Warning: molecule failed filter: reason cyano_imine_B(17) 107: v = { 107: 0,11}, 107: 1,12}, 107: 2,13}, 107: 3,14}, 107: 4,15}, 107: 5,10}, 107: 6,9}, 107: 7,8}, 107: 8,7}, 107: 9,6}, 107: 10,5}, 107: 11,17}, 107: 12,16}, 107: } 107: match = { 107: 0,11}, 107: 1,12}, 107: 2,13}, 107: 3,14}, 107: 4,15}, 107: 5,10}, 107: 6,9}, 107: 7,8}, 107: 8,7}, 107: 9,6}, 107: 10,5}, 107: 11,17}, 107: 12,16}, 107: } 107: Warning: molecule failed filter 107: Warning: molecule failed filter: reason keto_keto_gamma(5) 107: v = { 107: 0,0}, 107: 1,1}, 107: 2,2}, 107: 3,4}, 107: 4,5}, 107: 5,6}, 107: 6,7}, 107: 7,8}, 107: 8,9}, 107: 9,14}, 107: 10,15}, 107: 11,16}, 107: } 107: match = { 107: 0,0}, 107: 1,1}, 107: 2,2}, 107: 3,4}, 107: 4,5}, 107: 5,6}, 107: 6,7}, 107: 7,8}, 107: 8,9}, 107: 9,14}, 107: 10,15}, 107: 11,16}, 107: } 104: Finished 104: ----------------------- 104: testRootedSubgraphs 104: Finished 104: ----------------------- 104: testRootedPaths 104: Finished 96/235 Test #104: testSubgraphs1 ......................... Passed 0.40 sec test 108 Start 108: pyFilterCatalog 108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" 108: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap 108: Test timeout computed to be: 1500 106: Randomness seeded to: 4069095747 106: --------- 97/235 Test #103: pyTautomerQuery ........................ Passed 0.51 sec test 109 Start 109: testFragCatalog 109: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog 109: Test timeout computed to be: 1500 106: =============================================================================== 106: All tests passed (11 assertions in 1 test case) 106: 98/235 Test #106: subgraphsCatch ......................... Passed 0.30 sec test 110 Start 110: pyFragCatalog 110: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/Wrap/rough_test.py" 110: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap 110: Test timeout computed to be: 1500 109: 21 99/235 Test #107: filterCatalogTest ...................... Passed 0.35 sec test 111 Start 111: testDescriptors 111: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors 111: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 111: Test timeout computed to be: 1500 111: [15:23:12] ------------------------------------- 111: [15:23:12] Test Crippen parameter acquisition. 111: [15:23:12] done 111: [15:23:12] ------------------------------------- 111: [15:23:12] Test Crippen calculation. 111: [15:23:12] done 111: [15:23:12] ------------------------------------- 111: [15:23:12] Test Issue262: problems with Crippen calculation from pickles. 111: [15:23:12] done 111: [15:23:12] ------------------------------------- 111: [15:23:12] Test AMW calculation. 111: [15:23:12] done 111: [15:23:12] ------------------------------------- 111: [15:23:12] Test Exact MW calculation. 111: [15:23:12] done 111: [15:23:12] ------------------------------------- 111: [15:23:12] Test Labute ASA descriptors. 111: [15:23:12] done 111: [15:23:12] ------------------------------------- 111: [15:23:12] Test TPSA descriptors. 111: [15:23:12] done 111: [15:23:12] ------------------------------------- 111: [15:23:12] Test Lipinski parameters. 108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. 108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. 98: . 98: ---------------------------------------------------------------------- 98: Ran 11 tests in 1.294s 98: 98: OK 98: True 98: == CartesianProductStrategy CartesianProductStrategy 98: 197 out of 300 98: 0 6 out of 10 98: 1 3 out of 5 98: 2 4 out of 6 98: 198 out of 300 98: 0 10 out of 10 98: 1 5 out of 5 98: 2 6 out of 6 98: Skipped 10000000 in 0.07905292510986328 seconds 98: Skipped 10000000 in 0.6406230926513672 seconds 98: Skipped 10000000 in 0.16956377029418945 seconds 111: [15:23:13] done 111: [15:23:13] ------------------------------------- 111: [15:23:13] Test VSA descriptors. 111: [15:23:13] done 111: [15:23:13] ------------------------------------- 111: [15:23:13] Test molecular formula calculation. 111: [15:23:13] done 111: [15:23:13] ------------------------------------- 111: [15:23:13] Test Issue 3415534. 111: [15:23:13] done 111: [15:23:13] ------------------------------------- 111: [15:23:13] Test Issue3433771: Bad definition for Crippen atom type O11. 111: [15:23:13] done 111: [15:23:13] ------------------------------------- 111: [15:23:13] Test multithreading 111: reading molecules 110: ......... 110: ---------------------------------------------------------------------- 110: Ran 9 tests in 0.092s 110: 110: OK 111: processing 111: launch :0 111: launch :1 111: launch :2 111: launch :3 100/235 Test #98: pyChemReactionEnumerations ............. Passed 2.29 sec test 112 Start 112: testAUTOCORR2D 112: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D 112: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 112: Test timeout computed to be: 1500 109: [15:23:13] 109: 109: **** 109: Invariant Violation 109: nonsense 109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 109: Failed Expression: token != tokens.end() 109: ---------- 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 2# 0x0000FFFFB24C1948 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 4# 0x0000AAAADA5B7ADC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: 5# 0x0000AAAADA5B49E0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: 6# 0x0000FFFFB1A9229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 109: 8# 0x0000AAAADA5B4BB0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: 109: [15:23:13] 109: 109: **** 109: Invariant Violation 109: nonsense no new line 109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 109: Failed Expression: token != tokens.end() 109: ---------- 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 2# 0x0000FFFFB24C1948 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 4# 0x0000AAAADA5B7ADC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: 5# 0x0000AAAADA5B49E0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: 6# 0x0000FFFFB1A9229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 109: 8# 0x0000AAAADA5B4BB0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: 109: [15:23:13] 109: 109: **** 109: Invariant Violation 109: nonsense with tab 109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 109: Failed Expression: token != tokens.end() 109: ---------- 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 2# 0x0000FFFFB24C1948 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 4# 0x0000AAAADA5B7ADC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: 5# 0x0000AAAADA5B49E0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: 6# 0x0000FFFFB1A9229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 109: 8# 0x0000AAAADA5B4BB0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: 101/235 Test #109: testFragCatalog ........................ Passed 0.63 sec test 113 Start 113: testATF 113: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testATF 113: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 113: Test timeout computed to be: 1500 112: [15:23:13] ---------------------------- 112: start test autocorr2D 102/235 Test #113: testATF ................................ Passed 0.04 sec test 114 Start 114: testBCUT 114: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testBCUT 114: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 114: Test timeout computed to be: 1500 103/235 Test #110: pyFragCatalog .......................... Passed 0.66 sec test 115 Start 115: testEEM 115: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testEEM 115: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 115: Test timeout computed to be: 1500 114: [15:23:13] ------------------------------------- 114: [15:23:13] Basic BCUT tests. 114: [15:23:13] done 114: [15:23:13] ------------------------------------- 114: [15:23:13] Larger BCUT tests. 115: =>start test EEM 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 0 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 100 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 200 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 108: .............[15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] --- 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 108: [15:23:13] dasfsadf 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 108: .[15:23:13] SMILES Parse Error: syntax error while parsing: mydoghasfleas 108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: 108: [15:23:13] mydoghasfleas 108: [15:23:13] ^ 108: [15:23:13] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 29: All 191 tests passed 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 300 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 112: [15:23:13] done 112: [15:23:13] ------------------------------------- 112: [15:23:13] Test Github #3806: NaNs from AUTOCORR2D descriptor 112: [15:23:13] done 104/235 Test #112: testAUTOCORR2D ......................... Passed 0.74 sec test 116 Start 116: testPBF 116: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testPBF 116: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 116: Test timeout computed to be: 1500 29: 29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 75: [15:23:13] Finished: testSmiCorrectness() 75: [15:23:13] ----------------------------------------- 75: 75: [15:23:13] 75: ----------------------------------------- 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 116: [15:23:13] ------------------------------------- 116: [15:23:13] Basic PBF tests. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 75: [15:23:13] Spurious data before the first property will be ignored 75: [15:23:13] Property will be truncated after the first blank line 75: [15:23:13] Property will be truncated after the first blank line 75: [15:23:13] Property will be truncated after the first blank line 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 108: ....... 108: ---------------------------------------------------------------------- 108: Ran 21 tests in 1.069s 108: 108: OK 108: (Five aromatic carbons And (Not any of Five aromatic carbons)) 108: (Five aromatic carbons Or (Not any of Five aromatic carbons)) 108: (Not (Five aromatic carbons And (Not any of Five aromatic carbons))) 108: ******************************************** 108: Testing: PAINS_A 2 108: ******************************************** 108: Testing: PAINS_B 4 108: ******************************************** 108: Testing: PAINS_C 8 108: ******************************************** 108: Testing: PAINS 14 108: (Not FilterMatcher) 108: Bar 108: Count 1 108: ******************************************** 108: {'Cl,Br,I'} 108: 1 108: 2 108: running 115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 105/235 Test #108: pyFilterCatalog ........................ Passed 1.54 sec test 117 Start 117: testRDFcustom 117: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom 117: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 117: Test timeout computed to be: 1500 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 114: [15:23:14] ------------------------------------- 114: [15:23:14] Test empty molecule BCUT. 106/235 Test #114: testBCUT ............................... Passed 0.87 sec test 118 Start 118: testRDF 118: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDF 118: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 118: Test timeout computed to be: 1500 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 400 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 116: [15:23:14] done 116: [15:23:14] ------------------------------------- 116: [15:23:14] PBF edge cases. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 116: [15:23:14] done 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 107/235 Test #116: testPBF ................................ Passed 0.27 sec test 119 Start 119: testMORSE 119: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testMORSE 119: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 119: Test timeout computed to be: 1500 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: Elapsed time: 0.994021 s 115: Errors:0 115: [15:23:14] test on : 500 molecules done 108/235 Test #115: testEEM ................................ Passed 1.05 sec test 120 Start 120: test3D 120: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/test3D 120: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 120: Test timeout computed to be: 1500 120: [15:23:14] ------------------------------------- 120: [15:23:14] Basic PMI tests. 120: [15:23:14] done 120: [15:23:14] ------------------------------------- 120: [15:23:14] More PMI/NPR tests. 120: [15:23:14] done 120: [15:23:14] ------------------------------------- 120: [15:23:14] Basic NPR tests. 117: =>start test rdf custom 117: [15:23:14] test on : 365 molecules done 118: =>start test rdf 118: [15:23:14] test on : 365 molecules done 109/235 Test #118: testRDF ................................ Passed 0.66 sec test 121 Start 121: testWHIM 121: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testWHIM 121: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 121: Test timeout computed to be: 1500 120: [15:23:14] done 120: [15:23:14] ------------------------------------- 120: [15:23:14] PMI edge cases. 120: [15:23:14] done 120: [15:23:14] ------------------------------------- 120: [15:23:14] NPR edge cases. 120: [15:23:14] done 120: [15:23:14] ------------------------------------- 120: [15:23:14] 3D descriptors. 120: [15:23:14] done 120: [15:23:14] ------------------------------------- 120: [15:23:14] 3D descriptor edge cases. 120: [15:23:14] done 120: [15:23:14] ------------------------------------- 120: [15:23:14] Inertial shape factor. 120: [15:23:14] done 110/235 Test #120: test3D ................................. Passed 0.47 sec test 122 Start 122: testGETAWAY 122: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY 122: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 122: Test timeout computed to be: 1500 75: [15:23:14] Finished: testSDCorrectness() 75: [15:23:14] ----------------------------------------- 75: 111/235 Test #75: testMultithreadedMolSupplier ........... Passed 7.06 sec test 123 Start 123: testAUTOCORR3D 123: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D 123: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 123: Test timeout computed to be: 1500 119: =>start test MORSE 119: =>read file 119: [15:23:15] test on : 365 molecules done 112/235 Test #119: testMORSE .............................. Passed 0.94 sec test 124 Start 124: testCoulombMat 124: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat 124: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 124: Test timeout computed to be: 1500 124: ===================== Testing CoulombMat ======================= 121: =>start test WHIM 121: [15:23:15] test on : 365 molecules done 113/235 Test #121: testWHIM ............................... Passed 0.41 sec test 125 Start 125: descriptorsTestCatch 125: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch 125: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 125: Test timeout computed to be: 1500 124: CM test 1 mat Done 114/235 Test #124: testCoulombMat ......................... Passed 0.06 sec test 126 Start 126: pyMolDescriptors 126: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" 126: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap 126: Test timeout computed to be: 1500 125: Randomness seeded to: 3339088346 125: Warning: Atom Count for residue GLU5A does not match expected count 125: Warning: Atom Count for residue ASN39A does not match expected count 125: Warning: Atom Count for residue GLU53A does not match expected count 125: Warning: Atom Count for residue ARG64A does not match expected count 125: Warning: Atom Count for residue LYS80A does not match expected count 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test Issue252: Bad definitions for Crippen atom types. 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test calculation of ChiVs. 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test calculation of ChiNs. 125: Warning: Atom Count for residue GLU150A does not match expected count 125: Warning: Atom Count for residue ASN157A does not match expected count 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test calculation of HallKierAlpha. 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test calculation of Kappa1. 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test calculation of Kappa2. 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test calculation of Kappa3. 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test Crippen atom type calculations. 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test ring descriptors 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test other count descriptors. 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test MQN 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test GitHub Issue 56. 111: [15:23:15] WARNING: not removing hydrogen atom without neighbors 111: [15:23:15] WARNING: not removing hydrogen atom without neighbors 111: [15:23:15] WARNING: not removing hydrogen atom without neighbors 111: [15:23:15] WARNING: not removing hydrogen atom without neighbors 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test Github92: Bad Crippen atom type for pyrrole H. 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test Github362: order dependence in Kier-Hall descriptors. 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test calculation of spiro and bridgehead counts. 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test Github694: ExactMolWt ignoring the mass of the electron 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Testing Properties and KitchenSink 111: [15:23:15] ---Caught keyerror (bad property name)--- 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test USR Descriptor 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test Github #1973: support P and S terms for TPSA calculation 111: [15:23:15] done 111: [15:23:15] ------------------------------------- 111: [15:23:15] Test Github #2948: Empty molecule has non-zero LabuteASA 111: [15:23:15] done 123: =>start test autocorr3D 123: [15:23:15] test on : 365 molecules done 115/235 Test #111: testDescriptors ........................ Passed 2.66 sec 116/235 Test #123: testAUTOCORR3D ......................... Passed 0.43 sec test 127 Start 127: pyMolDescriptors3D 127: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap/test3D.py" 127: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap 127: Test timeout computed to be: 1500 test 128 Start 128: testFingerprints 128: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints 128: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 128: Test timeout computed to be: 1500 125: Warning: Atom Count for residue GLU5A does not match expected count 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: Atoms: 128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: 1 conj?: 1 128: 1 1->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: a conj?: 1 aromatic?: 1 128: 6 6->7 order: a conj?: 1 aromatic?: 1 128: 7 7->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: 1 conj?: 1 128: 9 8->10 order: a conj?: 1 aromatic?: 1 128: 10 10->1 order: a conj?: 1 aromatic?: 1 128: 11 7->3 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: SMI: Oc1cc2[nH]cnc2c(O)n1 128: Atoms: 128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: 1 conj?: 1 128: 1 1->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: a conj?: 1 aromatic?: 1 128: 6 6->7 order: a conj?: 1 aromatic?: 1 128: 7 7->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: 1 conj?: 1 128: 9 8->10 order: a conj?: 1 aromatic?: 1 128: 10 10->1 order: a conj?: 1 aromatic?: 1 128: 11 7->3 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: c1(O)cc2[nH]cnc2c(O)n1 128: Atoms: 128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: 1 conj?: 1 128: 1 0->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: a conj?: 1 aromatic?: 1 128: 6 6->7 order: a conj?: 1 aromatic?: 1 128: 7 7->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: 1 conj?: 1 128: 9 8->10 order: a conj?: 1 aromatic?: 1 128: 10 10->0 order: a conj?: 1 aromatic?: 1 128: 11 7->3 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: c1c(O)nc(O)c2c1[nH]cn2 128: Atoms: 128: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 3 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 5 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: a conj?: 1 aromatic?: 1 128: 1 1->2 order: 1 conj?: 1 128: 2 1->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: 1 conj?: 1 128: 5 4->6 order: a conj?: 1 aromatic?: 1 128: 6 6->7 order: a conj?: 1 aromatic?: 1 128: 7 7->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: a conj?: 1 aromatic?: 1 128: 9 9->10 order: a conj?: 1 aromatic?: 1 128: 10 7->0 order: a conj?: 1 aromatic?: 1 128: 11 10->6 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: c12cc(O)nc(O)c1nc[nH]2 128: Atoms: 128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 3 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: a conj?: 1 aromatic?: 1 128: 1 1->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: 1 conj?: 1 128: 3 2->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: 1 conj?: 1 128: 6 5->7 order: a conj?: 1 aromatic?: 1 128: 7 7->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: a conj?: 1 aromatic?: 1 128: 9 9->10 order: a conj?: 1 aromatic?: 1 128: 10 7->0 order: a conj?: 1 aromatic?: 1 128: 11 10->0 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: [nH]1c2cc(O)nc(O)c2nc1 128: Atoms: 128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 9 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 10 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: a conj?: 1 aromatic?: 1 128: 1 1->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: 1 conj?: 1 128: 4 3->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: a conj?: 1 aromatic?: 1 128: 6 6->7 order: 1 conj?: 1 128: 7 6->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: a conj?: 1 aromatic?: 1 128: 9 9->10 order: a conj?: 1 aromatic?: 1 128: 10 10->0 order: a conj?: 1 aromatic?: 1 128: 11 8->1 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: c1[nH]c2cc(O)nc(O)c2n1 128: Atoms: 128: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 1 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 5 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 8 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: a conj?: 1 aromatic?: 1 128: 1 1->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: 1 conj?: 1 128: 5 4->6 order: a conj?: 1 aromatic?: 1 128: 6 6->7 order: a conj?: 1 aromatic?: 1 128: 7 7->8 order: 1 conj?: 1 128: 8 7->9 order: a conj?: 1 aromatic?: 1 128: 9 9->10 order: a conj?: 1 aromatic?: 1 128: 10 10->0 order: a conj?: 1 aromatic?: 1 128: 11 9->2 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: n1c[nH]c2cc(O)nc(O)c21 128: Atoms: 128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 10 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: a conj?: 1 aromatic?: 1 128: 1 1->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: 1 conj?: 1 128: 6 5->7 order: a conj?: 1 aromatic?: 1 128: 7 7->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: 1 conj?: 1 128: 9 8->10 order: a conj?: 1 aromatic?: 1 128: 10 10->0 order: a conj?: 1 aromatic?: 1 128: 11 10->3 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: c12c(cc(O)nc1O)[nH]cn2 128: Atoms: 128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: a conj?: 1 aromatic?: 1 128: 1 1->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: 1 conj?: 1 128: 4 3->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: a conj?: 1 aromatic?: 1 128: 6 6->7 order: 1 conj?: 1 128: 7 1->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: a conj?: 1 aromatic?: 1 128: 9 9->10 order: a conj?: 1 aromatic?: 1 128: 10 6->0 order: a conj?: 1 aromatic?: 1 128: 11 10->0 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: c1(O)c2c(cc(O)n1)[nH]cn2 128: Atoms: 128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: 1 conj?: 1 128: 1 0->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: 1 conj?: 1 128: 6 5->7 order: a conj?: 1 aromatic?: 1 128: 7 3->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: a conj?: 1 aromatic?: 1 128: 9 9->10 order: a conj?: 1 aromatic?: 1 128: 10 7->0 order: a conj?: 1 aromatic?: 1 128: 11 10->2 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: Oc1c2c(cc(O)n1)[nH]cn2 128: Atoms: 128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: 1 conj?: 1 128: 1 1->2 order: a conj?: 1 aromatic?: 1 128: 2 2->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: 1 conj?: 1 128: 6 5->7 order: a conj?: 1 aromatic?: 1 128: 7 3->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: a conj?: 1 aromatic?: 1 128: 9 9->10 order: a conj?: 1 aromatic?: 1 128: 10 7->1 order: a conj?: 1 aromatic?: 1 128: 11 10->2 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: SMI: n1c(O)cc2[nH]cnc2c1O 128: Atoms: 128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 6 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 10 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: Bonds: 128: 0 0->1 order: a conj?: 1 aromatic?: 1 128: 1 1->2 order: 1 conj?: 1 128: 2 1->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: a conj?: 1 aromatic?: 1 128: 6 6->7 order: a conj?: 1 aromatic?: 1 128: 7 7->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: a conj?: 1 aromatic?: 1 128: 9 9->10 order: 1 conj?: 1 128: 10 9->0 order: a conj?: 1 aromatic?: 1 128: 11 8->4 order: a conj?: 1 aromatic?: 1 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: 128: 128: 128: 128: 128: 128: 128: 128: ------------------- 128: 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test Morgan Fingerprints. 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test Morgan Fingerprints using fromAtoms argument. 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test Morgan Fingerprints as bit vects. 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test Morgan Fingerprints with feature invariants. 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test additional Morgan fingerprints options. 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test Atom Codes. 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test Atom Pairs. 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test Atom Pairs part 2. 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test Topological Torsions. 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test Bulk Topological Torsions. 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: ..[15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: .[15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: ..[15:23:15] 126: 126: **** 125: Warning: Atom Count for residue ASN39A does not match expected count 117: =>start test morse custom 117: [15:23:15] test on : 365 molecules done 126: Pre-condition Violation 126: Number of atom props not equal to number of atoms 126: Violation occurred on line 89 in file ./Code/GraphMol/Descriptors/BCUT.cpp 126: Failed Expression: atom_props.size() == num_atoms 126: ---------- 126: Stacktrace: 126: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 126: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 126: 2# RDKit::Descriptors::BCUT2D(RDKit::ROMol const&, std::vector > const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitDescriptors.so.1 126: 3# 0x0000FFFF85E5D098 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so 126: 4# 0x0000FFFF85E71350 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so 126: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 126: 6# 0x0000FFFF89CD2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 126: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 126: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 126: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so 126: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 126: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 126: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 126: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 126: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 126: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 126: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 126: 17# 0x0000FFFF882AB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 126: 18# 0x0000FFFF882AB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 126: 19# 0x0000FFFF882AB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 126: 20# 0x0000FFFF882AB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 126: 21# 0x0000FFFF882AB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 126: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 126: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 126: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 126: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 126: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 126: 27# 0x0000FFFF89CCF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 126: 28# _PyObject_MakeTpCall in /usr/bin/python3 126: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 126: 30# 0x00000000005335D0 in /usr/bin/python3 126: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 126: 32# 0x00000000004AC3B4 in /usr/bin/python3 126: 33# 0x0000000000665934 in /usr/bin/python3 126: 34# _PyObject_MakeTpCall in /usr/bin/python3 126: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 126: 36# 0x00000000005335D0 in /usr/bin/python3 126: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 126: 38# 0x00000000004AC3B4 in /usr/bin/python3 126: 39# 0x0000000000665934 in /usr/bin/python3 126: 40# _PyObject_MakeTpCall in /usr/bin/python3 126: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 126: 42# 0x00000000005335D0 in /usr/bin/python3 126: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 126: 44# 0x00000000004AC3B4 in /usr/bin/python3 126: 45# 0x0000000000665934 in /usr/bin/python3 126: 46# _PyObject_MakeTpCall in /usr/bin/python3 126: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 126: 48# 0x0000000000505090 in /usr/bin/python3 126: 49# _PyObject_MakeTpCall in /usr/bin/python3 126: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 126: 51# PyEval_EvalCode in /usr/bin/python3 126: 52# 0x00000000005FFD24 in /usr/bin/python3 126: 53# 0x00000000005F9904 in /usr/bin/python3 126: 54# 0x0000000000627ED4 in /usr/bin/python3 126: 55# 0x0000000000627274 in /usr/bin/python3 126: 56# 0x0000000000627010 in /usr/bin/python3 126: 57# Py_RunMain in /usr/bin/python3 126: 58# Py_BytesMain in /usr/bin/python3 126: 59# 0x0000FFFF8A5D229C in /lib/aarch64-linux-gnu/libc.so.6 126: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 126: 61# _start in /usr/bin/python3 126: ---------- 126: **** 126: 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: ...Warning: Atom Count for residue GLU5A does not match expected count 126: Warning: Atom Count for residue ASN39A does not match expected count 126: Warning: Atom Count for residue GLU53A does not match expected count 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: Warning: Atom Count for residue ARG64A does not match expected count 126: Warning: Atom Count for residue LYS80A does not match expected count 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: Warning: Atom Count for residue GLU150A does not match expected count 126: Warning: Atom Count for residue ASN157A does not match expected count 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test Hashed Atom Pairs. 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test Hashed torsions. 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test Rooted Atom Pairs. 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test ignoring atoms in Atom Pairs. 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test Rooted Topological Torsions. 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test ignoring atoms in Topological Torsions. 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test atom info from morgan fingerprints. 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test atom info from morgan fingerprints including Info Redundant Environments. 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] ------------------------------------- 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] ------------------------------------- 125: Warning: Atom Count for residue GLU53A does not match expected count 128: [15:23:15] ------------------------------------- 128: [15:23:15] ------------------------------------- 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test Atom Pairs including info about chirality. 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test Topological Torsions including info about chirality. 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test GitHub Issue 25: fingerprint backwards compatibility. 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test GitHub Issue 151: PatternFingerprint problems 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test 3D atom pairs. 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule 128: [15:23:15] done 128: [15:23:15] ------------------------------------- 128: [15:23:15] Test multithreading with the pattern FP 128: reading molecules 126: Warning: Atom Count for residue GLU5A does not match expected count 125: Warning: Atom Count for residue ARG64A does not match expected count 128: pass 1 128: launch :0 128: launch :1 128: launch :2 128: launch :3 125: Warning: Atom Count for residue LYS80A does not match expected count 128: pass 2 128: launch :0 128: launch :1 128: launch :2 128: launch :3 117: =>start test AUTOCORR3D custom 117: [15:23:15] test on : 365 molecules done 127: ........ 127: ---------------------------------------------------------------------- 127: Ran 8 tests in 0.233s 127: 127: OK 126: Warning: Atom Count for residue ASN39A does not match expected count 117/235 Test #127: pyMolDescriptors3D ..................... Passed 0.87 sec test 129 Start 129: testMHFPFingerprint 129: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint 129: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 129: Test timeout computed to be: 1500 117: =>start test 2 WHIM custom 117: [15:23:16] test on : 365 molecules done 129: [15:23:16] ------------------------------------- 129: [15:23:16] Test MHFP fingerprint encoder initialization 129: [15:23:16] done 129: [15:23:16] ------------------------------------- 129: [15:23:16] Test MHFP shingling creation 126: Warning: Atom Count for residue GLU53A does not match expected count 129: [15:23:16] done 129: [15:23:16] ------------------------------------- 129: [15:23:16] Test MHFP hashing of string and uint arrays 129: [15:23:16] done 129: [15:23:16] ------------------------------------- 129: [15:23:16] Test SECFP fingerprint functionality 129: [15:23:16] done 118/235 Test #129: testMHFPFingerprint .................... Passed 0.12 sec test 130 Start 130: testFingerprintGenerators 130: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators 130: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 130: Test timeout computed to be: 1500 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test atom-pair fp generator 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test atom-pair fp generator with different arguments 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation 130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator 130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator 130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator 130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator 130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator 130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator 130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator 130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator 130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator 130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test atom-pair additional output 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test Folded Atom Pairs. 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test Rooted Atom Pairs. 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test ignoring atoms in Atom Pairs. 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test Atom Pairs including info about chirality. 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test Morgan Fingerprints. 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test morgan fp generator 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test Morgan Fingerprints using fromAtoms argument. 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test Morgan Fingerprints as bit vects. 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test Morgan Fingerprints with feature invariants. 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test additional Morgan fingerprints options. 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Single atoms setting radius 1 bits in Morgan fingerprints 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test different invariant generator combinations 126: Warning: Atom Count for residue ARG64A does not match expected count 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test invariant overriding 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test RDKit fp generator 125: Warning: Atom Count for residue GLU150A does not match expected count 117: =>start test 1 WHIM custom 117: [15:23:16] test on : 365 molecules done 125: Warning: Atom Count for residue ASN157A does not match expected count 126: Warning: Atom Count for residue LYS80A does not match expected count 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test unfolded version of RDKFP 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test topological torsion fp generator 130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test Topological Torsions. 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test Folded torsions. 130: [15:23:16] done 130: [15:23:16] ------------------------------------- 130: [15:23:16] Test Bulk Topological Torsions. 122: =>start test GETAWAY 122: [15:23:17] test on : 365 molecules done 119/235 Test #122: testGETAWAY ............................ Passed 2.33 sec test 131 Start 131: fpTestCatch 131: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch 131: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 131: Test timeout computed to be: 1500 130: [15:23:17] done 130: [15:23:17] ------------------------------------- 130: [15:23:17] Test Rooted Topological Torsions. 130: [15:23:17] done 130: [15:23:17] ------------------------------------- 130: [15:23:17] Test ignoring atoms in Topological Torsions. 130: [15:23:17] done 130: [15:23:17] ------------------------------------- 130: [15:23:17] ------------------------------------- 130: [15:23:17] Test Topological Torsions including info about chirality. 130: [15:23:17] done 130: [15:23:17] ------------------------------------- 130: [15:23:17] Test GitHub Issue 25: fingerprint backwards compatibility. 130: [15:23:17] done 130: [15:23:17] ------------------------------------- 130: [15:23:17] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. 130: [15:23:17] done 130: [15:23:17] ------------------------------------- 130: [15:23:17] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 130: [15:23:17] done 130: [15:23:17] ------------------------------------- 130: [15:23:17] Test convenience and bulk fp calculation functions 131: Randomness seeded to: 3867264887 131: =============================================================================== 131: All tests passed (188 assertions in 16 test cases) 131: 120/235 Test #131: fpTestCatch ............................ Passed 0.09 sec test 132 Start 132: fpGenTestCatch 132: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch 132: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 132: Test timeout computed to be: 1500 132: Randomness seeded to: 3045650141 132: =============================================================================== 132: All tests passed (2737 assertions in 7 test cases) 132: 121/235 Test #132: fpGenTestCatch ......................... Passed 0.22 sec test 133 Start 133: pyTestGenerator 133: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" 133: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 133: Test timeout computed to be: 1500 81: =============================================================================== 81: All tests passed (1601 assertions in 100 test cases) 81: 122/235 Test #81: fileParsersCatchTest ................... Passed 9.55 sec test 134 Start 134: pyTestMHFP 134: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" 134: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 134: Test timeout computed to be: 1500 29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 130: [15:23:17] done 130: [15:23:17] ------------------------------------- 130: [15:23:17] Test GitHub Issue #6958 130: [15:23:17] DEPRECATION WARNING: please use AtomPairGenerator 123/235 Test #130: testFingerprintGenerators .............. Passed 1.50 sec test 135 Start 135: testPartialCharges 135: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges 135: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges 135: Test timeout computed to be: 1500 124/235 Test #135: testPartialCharges ..................... Passed 0.07 sec test 136 Start 136: pyPartialCharges 136: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" 136: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap 136: Test timeout computed to be: 1500 126: Warning: Atom Count for residue GLU150A does not match expected count 126: Warning: Atom Count for residue ASN157A does not match expected count 29: All 191 tests passed 29: 29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... 133: .............. 133: ---------------------------------------------------------------------- 133: Ran 14 tests in 0.351s 133: 133: OK 134: .. 134: ---------------------------------------------------------------------- 134: Ran 2 tests in 0.043s 134: 134: OK 125/235 Test #133: pyTestGenerator ........................ Passed 1.13 sec test 137 Start 137: testMolTransforms 137: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 137: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms 137: Test timeout computed to be: 1500 126/235 Test #134: pyTestMHFP ............................. Passed 0.84 sec test 138 Start 138: molTransformsTestCatch 138: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch 138: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms 138: Test timeout computed to be: 1500 137: *********************************************************** 137: Testing MolTransforms 137: --------------------------------- 137: test1Canonicalization 137: 137: --------------------------------- 137: testGetSetBondLength 137: 137: --------------------------------- 137: testGetSetAngle 137: 137: --------------------------------- 137: testGetSetDihedral 137: 137: --------------------------------- 137: testGetSetDihedralThroughTripleBond 137: 137: --------------------------------- 137: testGithub1262: PMI descriptors incorrect 137: 137: --------------------------------- 137: testGithub1908: CanonicalizeMol() distorting bond lengths 137: 137: --------------------------------- 137: testGithub4302: native computeCanonicalTransform() generates non-canonical coords 137: 137: --------------------------------- 137: testWeightedCentroid 137: 137: *********************************************************** 127/235 Test #137: testMolTransforms ...................... Passed 0.11 sec test 139 Start 139: pyMolTransforms 139: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" 139: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap 139: Test timeout computed to be: 1500 138: Randomness seeded to: 1463548272 138: =============================================================================== 138: All tests passed (4 assertions in 1 test case) 138: 128/235 Test #138: molTransformsTestCatch ................. Passed 0.06 sec test 140 Start 140: forceFieldHelpersCatch 140: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch 140: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers 140: Test timeout computed to be: 1500 140: Randomness seeded to: 2495623965 140: =============================================================================== 140: All tests passed (17 assertions in 2 test cases) 140: 129/235 Test #140: forceFieldHelpersCatch ................. Passed 0.05 sec test 141 Start 141: testMMFFForceFieldHelpers 141: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers 141: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 141: Test timeout computed to be: 1500 141: [15:23:18] ------------------------------------- 141: [15:23:18] Test MMFF atom types. 141: [15:23:18] done 141: [15:23:18] ------------------------------------- 141: [15:23:18] Testing MMFF builder tools. 141: [15:23:18] done 141: [15:23:18] ------------------------------------- 141: [15:23:18] Testing MMFF builder+minimization. 141: [15:23:18] done 141: [15:23:18] ------------------------------------- 141: [15:23:18] Testing Issue239. 136: ....... 136: ---------------------------------------------------------------------- 136: Ran 7 tests in 0.290s 136: 136: OK 141: [15:23:18] done 141: [15:23:18] ------------------------------------- 141: [15:23:18] Testing calcEnergy with passed coords. 141: [15:23:18] done 141: [15:23:18] ------------------------------------- 141: [15:23:18] Testing calcGrad. 141: [15:23:19] done 141: [15:23:19] ------------------------------------- 141: [15:23:19] Testing Issue242. 141: [15:23:19] done 141: [15:23:19] ------------------------------------- 141: [15:23:19] Testing github 308: crash during MMFF parameterization . 141: [15:23:19] ------------------------------------- 141: [15:23:19] Testing SFIssue1653802. 141: [15:23:19] done 141: [15:23:19] ------------------------------------- 141: [15:23:19] Testing SFIssue2378119. 141: [15:23:19] done 141: [15:23:19] ------------------------------------- 141: [15:23:19] Test MMFF force-field parameter getters. 141: [15:23:19] ------------------------------------- 141: [15:23:19] Test MMFF multithreading 130/235 Test #136: pyPartialCharges ....................... Passed 1.15 sec test 142 Start 142: testMMFFForceFieldHelpersMultiThread 142: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 142: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 142: Test timeout computed to be: 1500 142: [15:23:19] ------------------------------------- 142: [15:23:19] Test MMFF multithreading 141: generating reference data 142: processing 142: launch :0 142: launch :1 142: launch :2 142: launch :3 142: launch :4 142: launch :5 142: launch :6 142: launch :7 142: launch :8 142: launch :9 142: launch :10 142: launch :11 142: launch :12 142: launch :13 142: launch :14 142: launch :15 142: launch :16 142: launch :17 142: launch :18 142: launch :19 142: launch :20 142: launch :21 142: launch :22 142: launch :23 142: done 142: [15:23:19] done 139: ........ 139: ---------------------------------------------------------------------- 139: Ran 8 tests in 0.250s 139: 139: OK 131/235 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.52 sec test 143 Start 143: testUFFForceFieldHelpers 143: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers 143: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF 143: Test timeout computed to be: 1500 117: =>start test GETAWAY custom 117: [15:23:19] test on : 365 molecules done 132/235 Test #117: testRDFcustom .......................... Passed 5.57 sec test 144 Start 144: testCrystalForceField 144: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField 144: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF 144: Test timeout computed to be: 1500 143: [15:23:19] ------------------------------------- 143: [15:23:19] Test UFF atom labels. 143: [15:23:19] done 143: [15:23:19] ------------------------------------- 143: [15:23:19] Test UFF atom typer. 143: [15:23:19] done 143: [15:23:19] ------------------------------------- 143: [15:23:19] Testing UFF builder tools. 143: [15:23:19] done 143: [15:23:19] ------------------------------------- 143: [15:23:19] Testing UFF builder+minimization. 144: ------------------------------------- 144: Test CrystalFF torsional term. 133/235 Test #139: pyMolTransforms ........................ Passed 1.06 sec test 145 Start 145: pyForceFieldHelpers 145: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" 145: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap 145: Test timeout computed to be: 1500 143: [15:23:19] done 143: [15:23:19] ------------------------------------- 143: [15:23:19] Testing UFF special cases. 143: [15:23:19] UFFTYPER: Unrecognized charge state for atom: 0 143: [15:23:19] done 143: [15:23:19] ------------------------------------- 143: [15:23:19] Testing Issue239. 143: [15:23:19] done 143: [15:23:19] ------------------------------------- 143: [15:23:19] Testing calcEnergy with passed coords. 143: [15:23:19] done 143: [15:23:19] ------------------------------------- 143: [15:23:19] Testing calcGrad. 143: [15:23:19] done 143: [15:23:19] ------------------------------------- 143: [15:23:19] Testing SFIssue1653802. 143: [15:23:19] done 143: [15:23:19] ------------------------------------- 143: [15:23:19] Testing SFIssue2378119. 143: [15:23:19] done 143: [15:23:19] ------------------------------------- 143: [15:23:19] Test UFF force-field parameter getters. 143: [15:23:19] ------------------------------------- 143: [15:23:19] Testing handling missing parameters. 143: [15:23:19] UFFTYPER: Unrecognized hybridization for atom: 0 143: [15:23:19] UFFTYPER: Unrecognized atom type: Cu+1 (0) 143: [15:23:19] UFFTYPER: Unrecognized hybridization for atom: 0 143: [15:23:19] UFFTYPER: Unrecognized atom type: Cu+1 (0) 143: [15:23:19] done 143: [15:23:19] ------------------------------------- 143: [15:23:19] Testing SFIssue3009337. 143: [15:23:19] done 143: [15:23:19] ------------------------------------- 143: [15:23:19] Test UFF multithreading 143: generating reference data 134/235 Test #144: testCrystalForceField .................. Passed 0.30 sec test 146 Start 146: testDistGeomHelpers 146: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 146: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers 146: Test timeout computed to be: 1500 128: [15:23:19] done 128: [15:23:19] ------------------------------------- 128: [15:23:19] Test GitHub Issue 258: Bad pattern fingerprint for query molecule 128: [15:23:19] done 128: [15:23:19] ------------------------------------- 128: [15:23:19] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. 128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:19] done 128: [15:23:19] ------------------------------------- 128: [15:23:19] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints 128: [15:23:19] done 128: [15:23:19] ------------------------------------- 128: [15:23:19] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:19] done 128: [15:23:19] ------------------------------------- 128: [15:23:19] Test unfolded version of RDKFP 128: [15:23:19] ------------------------------------- 128: [15:23:19] Test bitinfo of RDKFP 128: 562: [ 2 ], 128: 709: [ 0 1 ], 128: 1118: [ 0 1 2 ], 128: 1183: [ 1 2 ], 128: 1233: [ 0 1 2 ], 128: 1308: [ 0 ], [ 1 ], 128: 1339: [ 2 ], 128: 1728: [ 1 2 ], 128: 1772: [ 0 ], [ 1 ], 128: 1813: [ 0 1 ], 128: ------------ 128: [15:23:19] ------------------------------------- 128: [15:23:19] Single atoms setting radius 1 bits in Morgan fingerprints 128: [15:23:19] done 128: [15:23:19] ------------------------------------- 128: [15:23:19] Github #879: Pattern fingerprint should set bits for single-atom fragments. 128: [15:23:19] done 128: [15:23:19] ------------------------------------- 128: [15:23:19] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms 128: [15:23:19] done 128: [15:23:19] ------------------------------------- 128: [15:23:19] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False 128: [15:23:19] done 128: [15:23:19] ------------------------------------- 128: [15:23:19] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called 128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator 128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [15:23:19] done 128: [15:23:19] ------------------------------------- 128: [15:23:19] Github #2115: BitInfo not complete for RDKFingerprint 128: [15:23:19] done 128: [15:23:19] ------------------------------------- 128: [15:23:19] Github #3723: Fingerprint crash for mols with Zero order bonds 128: [15:23:19] done 135/235 Test #128: testFingerprints ....................... Passed 4.61 sec test 147 Start 147: distGeomHelpersCatch 147: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch 147: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers 147: Test timeout computed to be: 1500 146: [15:23:19] ******************************************************** 146: [15:23:19] Testing DistGeomHelpers 146: [15:23:19] --------------------------------- 146: [15:23:19] test2 146: 146: go 146: ------------------------------------- 146: 141: processing 141: launch :0 141: launch :1 141: launch :2 141: launch :3 147: Randomness seeded to: 2602053797 141: [15:23:20] Rep: 0 Mol:0 141: [15:23:20] Rep: 0 Mol:3 141: [15:23:20] Rep: 0 Mol:2 141: [15:23:20] Rep: 0 Mol:4 141: [15:23:20] Rep: 0 Mol:1 141: [15:23:20] Rep: 0 Mol:5 141: [15:23:20] Rep: 0 Mol:8 141: [15:23:20] Rep: 0 Mol:9 141: [15:23:20] Rep: 0 Mol:13 147: [15:23:20] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [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)] 141: [15:23:20] Rep: 0 Mol:12 141: [15:23:20] Rep: 0 Mol:6 141: [15:23:20] Rep: 0 Mol:16 141: [15:23:20] Rep: 0 Mol:10 141: [15:23:20] Rep: 0 Mol:17 147: [15:23:20] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [15:23:20] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [15:23:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [15:23:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [15:23:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [15:23:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [15:23:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [15:23:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 147: [15:23:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 147: [15:23:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 147: [15:23:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 147: [15:23:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 147: [15:23:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 147: [15:23:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 147: [15:23:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, [(1 -1), (1 -0.5), (1 -0.2), (1 -0.3), (1 0), (1 -0.3)] 147: [15:23:20] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, [(1 0), (1 3.6), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 147: [15:23:20] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [15:23:20] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [15:23:20] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 147: [15:23:20] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 147: [15:23:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [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)] 141: [15:23:20] Rep: 0 Mol:20 147: ----------- 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [15:23:20] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 147: [15:23:20] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 147: [15:23:20] [!#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)] 141: [15:23:20] Rep: 0 Mol:24 141: [15:23:20] Rep: 0 Mol:7 141: [15:23:20] Rep: 0 Mol:28 147: [15:23:20] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] 147: ----------- 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 147: [15:23:20] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] 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)] 141: [15:23:20] Rep: 0 Mol:11 141: [15:23:20] Rep: 0 Mol:15 147: ----------- 147: ----------- 141: [15:23:20] Rep: 0 Mol:19 141: [15:23:20] Rep: 0 Mol:21 141: [15:23:20] Rep: 0 Mol:23 141: [15:23:20] Rep: 0 Mol:27 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 147: [15:23:20] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 147: [15:23:20] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 147: [15:23:20] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 147: [15:23:20] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 147: [15:23:20] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 147: [15:23:20] [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)] 141: [15:23:20] Rep: 0 Mol:31 145: [15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 145: [15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 145: [15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 145: [15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 145: [15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 141: [15:23:20] Rep: 0 Mol:25 145: ..[15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 145: .[15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 141: [15:23:20] Rep: 0 Mol:29 141: [15:23:20] Rep: 0 Mol:14 145: .[15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 143: processing 143: launch :0 143: launch :1 143: launch :2 143: launch :3 143: [15:23:20] Rep: 0 Mol:2 141: [15:23:20] Rep: 0 Mol:18 143: [15:23:20] Rep: 0 Mol:0 143: [15:23:20] Rep: 0 Mol:4 143: [15:23:20] Rep: 0 Mol:1 143: [15:23:20] Rep: 0 Mol:5 143: [15:23:20] Rep: 0 Mol:9 143: [15:23:20] Rep: 0 Mol:6 143: [15:23:20] Rep: 0 Mol:10 143: [15:23:20] Rep: 0 Mol:3 141: [15:23:20] Rep: 0 Mol:22 143: [15:23:20] Rep: 0 Mol:13 145: .[15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 143: [15:23:20] Rep: 0 Mol:8 143: [15:23:20] Rep: 0 Mol:12 143: [15:23:20] Rep: 0 Mol:16 143: [15:23:20] Rep: 0 Mol:17 141: [15:23:20] Rep: 0 Mol:26 143: [15:23:20] Rep: 0 Mol:14 145: .[15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 143: [15:23:20] Rep: 0 Mol:20 143: [15:23:20] Rep: 0 Mol:18 143: [15:23:20] Rep: 0 Mol:24 143: [15:23:20] Rep: 0 Mol:28 143: [15:23:20] Rep: 0 Mol:7 143: [15:23:20] Rep: 0 Mol:22 143: [15:23:20] Rep: 0 Mol:11 143: [15:23:20] Rep: 0 Mol:15 143: [15:23:20] Rep: 0 Mol:26 147: [15:23:20] UFFTYPER: Unrecognized atom type: Pt5+2 (1) 141: [15:23:20] Rep: 0 Mol:30 143: [15:23:20] Rep: 0 Mol:21 145: .[15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 145: .[15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 143: [15:23:20] Rep: 0 Mol:19 143: [15:23:20] Rep: 0 Mol:30 143: [15:23:20] Rep: 0 Mol:23 143: [15:23:20] Rep: 0 Mol:27 143: [15:23:20] Rep: 0 Mol:25 145: .[15:23:20] UFFTYPER: Unrecognized hybridization for atom: 0 145: [15:23:20] UFFTYPER: Unrecognized atom type: Cu+1 (0) 145: .[15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 145: [15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 145: [15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 145: [15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 145: [15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 147: [15:23:20] UFFTYPER: Unrecognized charge state for atom: 1 145: .[15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 145: .[15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 145: .[15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 145: ...[15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 143: [15:23:20] Rep: 0 Mol:29 143: [15:23:20] Rep: 0 Mol:31 147: [15:23:20] UFFTYPER: Unrecognized charge state for atom: 1 147: [15:23:20] UFFTYPER: Unrecognized charge state for atom: 1 141: [15:23:20] Rep: 20 Mol:0 141: [15:23:20] Rep: 20 Mol:4 141: [15:23:20] Rep: 20 Mol:8 141: [15:23:20] Rep: 20 Mol:12 141: [15:23:20] Rep: 20 Mol:16 141: [15:23:20] Rep: 20 Mol:20 141: [15:23:20] Rep: 20 Mol:24 141: [15:23:20] Rep: 20 Mol:28 145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 141: [15:23:20] Rep: 20 Mol:3 141: [15:23:20] Rep: 20 Mol:7 141: [15:23:20] Rep: 20 Mol:11 141: [15:23:20] Rep: 20 Mol:15 141: [15:23:20] Rep: 20 Mol:19 141: [15:23:20] Rep: 20 Mol:23 141: [15:23:20] Rep: 20 Mol:27 141: [15:23:20] Rep: 20 Mol:31 145: ... 145: ---------------------------------------------------------------------- 145: Ran 19 tests in 0.281s 145: 145: OK 147: [15:23:20] UFFTYPER: Unrecognized charge state for atom: 5 147: [15:23:20] UFFTYPER: Unrecognized charge state for atom: 5 141: [15:23:20] Rep: 20 Mol:1 141: [15:23:20] Rep: 20 Mol:5 141: [15:23:20] Rep: 20 Mol:9 141: [15:23:20] Rep: 20 Mol:13 141: [15:23:20] Rep: 20 Mol:17 141: [15:23:20] Rep: 20 Mol:21 141: [15:23:20] Rep: 20 Mol:25 141: [15:23:20] Rep: 20 Mol:29 147: [15:23:20] UFFTYPER: Unrecognized charge state for atom: 5 141: [15:23:20] Rep: 40 Mol:0 141: [15:23:20] Rep: 40 Mol:4 136/235 Test #145: pyForceFieldHelpers .................... Passed 0.94 sec test 148 Start 148: pyDistGeomHelpers 148: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" 148: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 148: Test timeout computed to be: 1500 141: [15:23:20] Rep: 40 Mol:3 141: [15:23:20] Rep: 40 Mol:7 141: [15:23:20] Rep: 40 Mol:11 141: [15:23:20] Rep: 40 Mol:15 141: [15:23:20] Rep: 40 Mol:19 141: [15:23:20] Rep: 40 Mol:23 141: [15:23:20] Rep: 40 Mol:27 141: [15:23:20] Rep: 40 Mol:31 141: [15:23:20] Rep: 40 Mol:8 141: [15:23:20] Rep: 40 Mol:12 141: [15:23:20] Rep: 40 Mol:16 141: [15:23:20] Rep: 40 Mol:20 141: [15:23:20] Rep: 40 Mol:24 141: [15:23:20] Rep: 40 Mol:28 147: [15:23:20] UFFTYPER: Unrecognized charge state for atom: 6 147: [15:23:20] UFFTYPER: Unrecognized charge state for atom: 6 147: [15:23:20] UFFTYPER: Unrecognized charge state for atom: 6 141: [15:23:20] Rep: 20 Mol:2 141: [15:23:20] Rep: 20 Mol:6 141: [15:23:20] Rep: 20 Mol:10 141: [15:23:20] Rep: 20 Mol:14 141: [15:23:20] Rep: 20 Mol:18 141: [15:23:20] Rep: 20 Mol:22 141: [15:23:20] Rep: 20 Mol:26 141: [15:23:20] Rep: 20 Mol:30 141: [15:23:20] Rep: 40 Mol:1 141: [15:23:20] Rep: 40 Mol:5 141: [15:23:20] Rep: 40 Mol:9 141: [15:23:20] Rep: 40 Mol:13 141: [15:23:20] Rep: 40 Mol:17 141: [15:23:20] Rep: 40 Mol:21 141: [15:23:20] Rep: 40 Mol:25 141: [15:23:20] Rep: 40 Mol:29 143: [15:23:20] Rep: 100 Mol:0 143: [15:23:20] Rep: 100 Mol:4 143: [15:23:20] Rep: 100 Mol:8 143: [15:23:20] Rep: 100 Mol:12 143: [15:23:20] Rep: 100 Mol:16 141: [15:23:20] Rep: 60 Mol:3 143: [15:23:20] Rep: 100 Mol:20 143: [15:23:20] Rep: 100 Mol:24 143: [15:23:20] Rep: 100 Mol:28 141: [15:23:20] Rep: 60 Mol:7 141: [15:23:20] Rep: 60 Mol:11 141: [15:23:20] Rep: 60 Mol:15 141: [15:23:20] Rep: 60 Mol:19 141: [15:23:20] Rep: 60 Mol:23 141: [15:23:20] Rep: 60 Mol:27 141: [15:23:20] Rep: 60 Mol:31 143: [15:23:20] Rep: 100 Mol:3 143: [15:23:20] Rep: 100 Mol:7 143: [15:23:20] Rep: 100 Mol:11 143: [15:23:20] Rep: 100 Mol:15 143: [15:23:20] Rep: 100 Mol:19 143: [15:23:20] Rep: 100 Mol:23 143: [15:23:20] Rep: 100 Mol:27 143: [15:23:20] Rep: 100 Mol:31 141: [15:23:20] Rep: 60 Mol:0 141: [15:23:20] Rep: 60 Mol:4 141: [15:23:20] Rep: 60 Mol:8 141: [15:23:20] Rep: 60 Mol:12 141: [15:23:20] Rep: 60 Mol:16 141: [15:23:20] Rep: 60 Mol:20 141: [15:23:20] Rep: 60 Mol:24 141: [15:23:20] Rep: 60 Mol:28 141: [15:23:20] Rep: 40 Mol:2 141: [15:23:20] Rep: 40 Mol:6 141: [15:23:20] Rep: 40 Mol:10 141: [15:23:20] Rep: 40 Mol:14 141: [15:23:20] Rep: 40 Mol:18 141: [15:23:20] Rep: 40 Mol:22 141: [15:23:20] Rep: 40 Mol:26 141: [15:23:20] Rep: 40 Mol:30 143: [15:23:20] Rep: 100 Mol:1 143: [15:23:20] Rep: 100 Mol:5 143: [15:23:20] Rep: 100 Mol:9 143: [15:23:20] Rep: 100 Mol:13 143: [15:23:20] Rep: 100 Mol:17 143: [15:23:20] Rep: 100 Mol:21 143: [15:23:20] Rep: 100 Mol:25 143: [15:23:20] Rep: 100 Mol:29 141: [15:23:21] Rep: 80 Mol:3 141: [15:23:21] Rep: 80 Mol:7 141: [15:23:21] Rep: 80 Mol:11 141: [15:23:21] Rep: 80 Mol:15 141: [15:23:21] Rep: 80 Mol:19 141: [15:23:21] Rep: 80 Mol:23 141: [15:23:21] Rep: 60 Mol:1 141: [15:23:21] Rep: 60 Mol:5 141: [15:23:21] Rep: 60 Mol:9 141: [15:23:21] Rep: 60 Mol:13 141: [15:23:21] Rep: 60 Mol:17 141: [15:23:21] Rep: 60 Mol:21 141: [15:23:21] Rep: 60 Mol:25 141: [15:23:21] Rep: 60 Mol:29 141: [15:23:21] Rep: 80 Mol:27 141: [15:23:21] Rep: 80 Mol:31 141: [15:23:21] Rep: 80 Mol:0 141: [15:23:21] Rep: 80 Mol:4 141: [15:23:21] Rep: 80 Mol:8 141: [15:23:21] Rep: 60 Mol:2 141: [15:23:21] Rep: 60 Mol:6 141: [15:23:21] Rep: 60 Mol:10 141: [15:23:21] Rep: 60 Mol:14 141: [15:23:21] Rep: 60 Mol:18 141: [15:23:21] Rep: 80 Mol:12 141: [15:23:21] Rep: 80 Mol:16 141: [15:23:21] Rep: 80 Mol:20 141: [15:23:21] Rep: 80 Mol:24 141: [15:23:21] Rep: 80 Mol:28 141: [15:23:21] Rep: 60 Mol:22 141: [15:23:21] Rep: 60 Mol:26 141: [15:23:21] Rep: 60 Mol:30 143: [15:23:21] Rep: 100 Mol:2 143: [15:23:21] Rep: 100 Mol:6 143: [15:23:21] Rep: 100 Mol:10 143: [15:23:21] Rep: 100 Mol:14 143: [15:23:21] Rep: 100 Mol:18 143: [15:23:21] Rep: 100 Mol:22 143: [15:23:21] Rep: 100 Mol:26 143: [15:23:21] Rep: 100 Mol:30 141: [15:23:21] Rep: 80 Mol:1 141: [15:23:21] Rep: 80 Mol:5 141: [15:23:21] Rep: 80 Mol:9 141: [15:23:21] Rep: 80 Mol:13 141: [15:23:21] Rep: 80 Mol:17 141: [15:23:21] Rep: 80 Mol:21 141: [15:23:21] Rep: 80 Mol:25 141: [15:23:21] Rep: 80 Mol:29 148: .[15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 95: 0,0 0 95: 0,1 0 95: 1,0 0 95: 1,1 0 95: 2,0 0 95: 2,1 0 141: [15:23:21] Rep: 80 Mol:2 137/235 Test #95: testEnumeration ........................ Passed 10.85 sec test 149 Start 149: testMolAlign 149: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 149: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign 149: Test timeout computed to be: 1500 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 141: [15:23:21] Rep: 80 Mol:6 141: [15:23:21] Rep: 80 Mol:10 141: [15:23:21] Rep: 80 Mol:14 141: [15:23:21] Rep: 80 Mol:18 141: [15:23:21] Rep: 80 Mol:22 141: [15:23:21] Rep: 80 Mol:26 141: [15:23:21] Rep: 80 Mol:30 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: ..[15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: ..[15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: .[15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 149: *********************************************************** 149: Testing MolAlign 149: --------------------------------- 149: test1MolAlign 149: 149: --------------------------------- 149: test1GetBestRMS 149: 149: --------------------------------- 149: test1MolWithQueryAlign 149: 149: --------------------------------- 149: test2AtomMap 149: 149: --------------------------------- 149: test3Weights 149: 149: --------------------------------- 149: testIssue241 149: 149: *********************************************************** 138/235 Test #149: testMolAlign ........................... Passed 0.14 sec test 150 Start 150: testO3AAlign 150: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign 150: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign 150: Test timeout computed to be: 1500 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 141: [15:23:21] done 141: [15:23:21] ------------------------------------- 141: [15:23:21] Test MMFF multithreading2 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 143: [15:23:21] done 143: [15:23:21] ------------------------------------- 143: [15:23:21] Test UFF multithreading2 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [15:23:19] --------------------------------- 146: [15:23:19] test3 146: 146: [15:23:20] --------------------------------- 146: [15:23:20] test4 146: 146: [15:23:20] --------------------------------- 146: [15:23:20] test5 146: 146: [15:23:21] --------------------------------- 146: [15:23:21] test6 146: 146: [15:23:21] --------------------------------- 146: [15:23:21] test15Dists 146: 146: [15:23:21] --------------------------------- 146: [15:23:21] test Issue 215 146: 146: [15:23:21] --------------------------------- 146: [15:23:21] testMultipleConfs 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] testMultipleConfsExpTors 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] testIssue227 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] testIssue236 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] testOrdering 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] testIssue244 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] testIssue251 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] testIssue276 146: [15:23:22] --------------------------------- 146: [15:23:22] testIssue284 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] testIssue285 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] testIssue355 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] testRandomCoords 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] test sf.net issue 1989539 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] test sf.net issue 2091864 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] test constrained embedding 146: 146: [15:23:22] ssd: 0.0752641 147: [15:23:22] UFFTYPER: Warning: hybridization set to SP3 for atom 6 146: [15:23:22] ssd: 0.0659363 148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() 125: Warning: Atom Count for residue GLU5A does not match expected count 125: Warning: Atom Count for residue ASN39A does not match expected count 125: Warning: Atom Count for residue GLU53A does not match expected count 125: Warning: Atom Count for residue ARG64A does not match expected count 125: Warning: Atom Count for residue LYS80A does not match expected count 148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() 125: Warning: Atom Count for residue GLU150A does not match expected count 125: Warning: Atom Count for residue ASN157A does not match expected count 148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() 125: =============================================================================== 125: All tests passed (515 assertions in 10 test cases) 125: 139/235 Test #125: descriptorsTestCatch ................... Passed 7.18 sec test 151 Start 151: molAlignCatchTest 151: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest 151: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign 151: Test timeout computed to be: 1500 147: [15:23:22] UFFTYPER: Warning: hybridization set to SP3 for atom 6 148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() 141: [15:23:22] done 141: [15:23:22] ------------------------------------- 141: [15:23:22] Test MMFF multithreading3 148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() 151: Randomness seeded to: 3060517926 151: 45995120 148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() 147: [15:23:22] UFFTYPER: Warning: hybridization set to SP3 for atom 6 148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [15:23:22] --------------------------------- 146: [15:23:22] test sf.net issue 2091974 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] test sf.net issue 2835784 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] test sf.net issue 3019283 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] test sf.net issue 3238580 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] test sf.net issue 3483968 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] test github issue 55 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] test1 146: 146: [15:23:22] --------------------------------- 146: [15:23:22] test multi-threading 146: 146: building molecules 151: 72542480 148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() 143: [15:23:22] done 143: [15:23:22] ------------------------------------- 143: [15:23:22] Test UFF multithreading3 146: generating reference data 148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() 147: [15:23:22] UFFTYPER: Warning: hybridization set to SP3 for atom 11 147: [15:23:22] UFFTYPER: Warning: hybridization set to SP3 for atom 11 148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() 147: [15:23:22] UFFTYPER: Warning: hybridization set to SP3 for atom 11 148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() 148: .[15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:23:23] Molecule does not have explicit Hs. Consider calling AddHs() 141: [15:23:23] done 141: [15:23:23] ------------------------------------- 141: [15:23:23] Testing github 162: Incorrect SMILES after MMFF parameterization . 141: [15:23:23] done 141: [15:23:23] ------------------------------------- 141: [15:23:23] Testing github 224: crash during MMFF parameterization . 141: [15:23:23] done 141: [15:23:23] ------------------------------------- 141: [15:23:23] Testing github6728: crash due to missing stretch-bend params. 140/235 Test #141: testMMFFForceFieldHelpers .............. Passed 4.47 sec test 152 Start 152: pyMolAlign 152: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" 152: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap 152: Test timeout computed to be: 1500 143: [15:23:23] done 143: [15:23:23] ------------------------------------- 143: [15:23:23] Testing GitHubIssue62. 148: [15:23:23] Molecule does not have explicit Hs. Consider calling AddHs() 143: [15:23:23] beta-lactam 39.6387 143: [15:23:23] cyclopropanone 174.698 143: [15:23:23] aziridine 337.986 143: [15:23:23] aziridinone 115.248 143: [15:23:23] isobutene 2.48217 143: [15:23:23] acetone 1.91788 143: [15:23:23] cyclopentanone 10.1648 143: [15:23:23] cyclopropene 99.4921 143: [15:23:23] cyclobutene 41.0156 143: [15:23:23] cyclopropane 267.236 143: [15:23:23] gamma-lactam 15.7471 143: [15:23:23] trans-2,3-diphenylcyclopropan-1-one 203.398 143: [15:23:23] cis-2,3-diphenylcyclopropan-1-one 206.852 143: [15:23:23] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 143: [15:23:23] cyclopropylidencyclobutane 218.879 143: [15:23:23] diphenylmethylidencyclobutane 79.6139 143: [15:23:23] done 143: [15:23:23] ------------------------------------- 143: [15:23:23] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. 143: [15:23:23] done 143: [15:23:23] ------------------------------------- 143: [15:23:23] Test square planar complexes 143: [15:23:23] done 143: [15:23:23] ------------------------------------- 143: [15:23:23] Test octahedral complexes 143: [15:23:23] done 141/235 Test #143: testUFFForceFieldHelpers ............... Passed 3.85 sec test 153 Start 153: testFeatures 153: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures 153: Test timeout computed to be: 1500 153: [15:23:23] ------------------------------------- 153: [15:23:23] AtomType parser testing. 153: [15:23:23] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] 153: [15:23:23] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' 153: [15:23:23] done 153: [15:23:23] ------------------------------------- 153: [15:23:23] FeatureDefinition parser testing. 153: [15:23:23] done 153: [15:23:23] ------------------------------------- 153: [15:23:23] Test pulling feat defs from a string. 153: [15:23:23] done 153: [15:23:23] ------------------------------------- 153: [15:23:23] FeatureDef functionality testing. 153: [15:23:23] done 153: [15:23:23] ------------------------------------- 153: [15:23:23] FeatureFactory testing. 153: [15:23:23] 1 153: [15:23:23] 2 153: [15:23:23] 3 153: [15:23:23] 4 153: [15:23:23] 5 153: [15:23:23] 6 153: [15:23:23] done 153: [15:23:23] ------------------------------------- 153: [15:23:23] Feature Location testing. 153: [15:23:23] done 153: [15:23:23] ------------------------------------- 153: [15:23:23] Test building a FeatureFactory from a file 153: [15:23:23] done 153: [15:23:23] ------------------------------------- 153: [15:23:23] Testing Issue 224. 153: [15:23:23] done 153: [15:23:23] ------------------------------------- 153: [15:23:23] Testing Issue 225. 153: [15:23:23] done 153: [15:23:23] ------------------------------------- 153: [15:23:23] Test Issue346 153: [15:23:23] done 153: [15:23:23] ------------------------------------- 153: [15:23:23] Test Issue347 153: [15:23:23] done 153: [15:23:23] ------------------------------------- 153: [15:23:23] Testing Issue 348. 153: [15:23:23] SMARTS Parse Error: syntax error while parsing: [C[C] 153: [15:23:23] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' 153: [15:23:23] ------------------------------------- 153: [15:23:23] Testing Nested AtomType definitions. 153: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] 153: [15:23:23] ------------------------------------- 153: [15:23:23] Testing Github Issue #252: crash when calling getPos() with no conformer. 153: [15:23:23] expect a precondition failure message below 153: [15:23:23] 153: 153: **** 153: Pre-condition Violation 153: molecule has no conformers 153: Violation occurred on line 37 in file ./Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp 153: Failed Expression: dp_mol->getNumConformers() 153: ---------- 153: Stacktrace: 153: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 153: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 153: 2# RDKit::MolChemicalFeature::getPos(int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 153: 3# RDKit::MolChemicalFeature::getPos() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 153: 4# 0x0000AAAAD3C51AB0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: 5# 0x0000AAAAD3C44568 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: 6# 0x0000FFFFA541229C in /lib/aarch64-linux-gnu/libc.so.6 153: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 153: 8# 0x0000AAAAD3C44730 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: ---------- 153: **** 153: 153: [15:23:23] Done 153: [15:23:23] ------------------------------------- 153: [15:23:23] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() 153: [15:23:23] done 142/235 Test #153: testFeatures ........................... Passed 0.06 sec test 154 Start 154: pyChemicalFeatures 154: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" 154: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 154: Test timeout computed to be: 1500 148: [15:23:23] Molecule does not have explicit Hs. Consider calling AddHs() 52: Randomness seeded to: 1674199327 52: =============================================================================== 52: All tests passed (14835 assertions in 14 test cases) 52: 143/235 Test #52: canonTestsCatch ........................ Passed 18.46 sec test 155 Start 155: testShapeHelpers 155: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers 155: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers 155: Test timeout computed to be: 1500 155: *********************************************************** 155: Testing ShapeHelpers 155: --------------------------------- 155: test1Encode 155: 155: --------------------------------- 155: test2Compare 155: 155: --------------------------------- 155: testGithub4364 155: 155: *********************************************************** 144/235 Test #155: testShapeHelpers ....................... Passed 0.05 sec test 156 Start 156: pyShapeHelpers 156: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" 156: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap 156: Test timeout computed to be: 1500 126: Warning: Atom Count for residue GLU5A does not match expected count 126: Warning: Atom Count for residue ASN39A does not match expected count 126: Warning: Atom Count for residue GLU53A does not match expected count 126: Warning: Atom Count for residue ARG64A does not match expected count 126: Warning: Atom Count for residue LYS80A does not match expected count 126: Warning: Atom Count for residue GLU150A does not match expected count 126: Warning: Atom Count for residue ASN157A does not match expected count 126: .[15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: .[15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: ..[15:23:23] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:23] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:23] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:23] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:23] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:23] DEPRECATION WARNING: please use AtomPairGenerator 126: .[15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: ...[15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator 126: ....[15:23:23] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:23] DEPRECATION WARNING: please use AtomPairGenerator 126: ....[15:23:23] DEPRECATION WARNING: please use AtomPairGenerator 126: [15:23:23] DEPRECATION WARNING: please use AtomPairGenerator 126: .[15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: ..[15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: .[15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: ... 126: ---------------------------------------------------------------------- 126: Ran 31 tests in 8.276s 126: 126: OK 126: exactmw 78.046950192 126: amw 78.11399999999999 126: lipinskiHBA 0.0 126: lipinskiHBD 0.0 126: NumRotatableBonds 0.0 126: NumHBD 0.0 126: NumHBA 0.0 126: NumHeavyAtoms 6.0 126: NumAtoms 12.0 126: NumHeteroatoms 0.0 126: NumAmideBonds 0.0 126: FractionCSP3 0.0 126: NumRings 1.0 126: NumAromaticRings 1.0 126: NumAliphaticRings 0.0 126: NumSaturatedRings 0.0 126: NumHeterocycles 0.0 126: NumAromaticHeterocycles 0.0 126: NumSaturatedHeterocycles 0.0 126: NumAliphaticHeterocycles 0.0 126: NumSpiroAtoms 0.0 126: NumBridgeheadAtoms 0.0 126: NumAtomStereoCenters 0.0 126: NumUnspecifiedAtomStereoCenters 0.0 126: labuteASA 37.43140311949697 126: tpsa 0.0 126: CrippenClogP 1.6866 126: CrippenMR 26.441999999999993 126: chi0v 3.464101615137755 126: chi1v 2.0000000000000004 126: chi2v 0.6666666666666671 126: chi3v 0.6666666666666671 126: chi4v 0.38490017945975075 126: chi0n 3.464101615137755 126: chi1n 2.0000000000000004 126: chi2n 0.6666666666666671 126: chi3n 0.6666666666666671 126: chi4n 0.38490017945975075 126: hallKierAlpha -0.78 126: kappa1 3.4115708812260532 126: kappa2 1.6057694396735218 126: kappa3 0.5823992601400448 126: Phi 0.9130327103921437 126: CustomNumAtoms 6.0 126: exactmw 78.046950192 126: lipinskiHBA 0.0 148: [15:23:23] Molecule does not have explicit Hs. Consider calling AddHs() 154: .[15:23:23] Molecule does not have explicit Hs. Consider calling AddHs() 154: .[15:23:23] Molecule does not have explicit Hs. Consider calling AddHs() 145/235 Test #126: pyMolDescriptors ....................... Passed 8.80 sec test 157 Start 157: testMolCatalog 157: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 157: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog 157: Test timeout computed to be: 1500 146/235 Test #157: testMolCatalog ......................... Passed 0.04 sec test 158 Start 158: pyMolCatalog 158: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 158: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 158: Test timeout computed to be: 1500 148: [15:23:24] Molecule does not have explicit Hs. Consider calling AddHs() 154: ..[15:23:24] Molecule does not have explicit Hs. Consider calling AddHs() 154: .[15:23:24] Molecule does not have explicit Hs. Consider calling AddHs() 154: .[15:23:24] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] 154: [15:23:24] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' 154: ... 154: ---------------------------------------------------------------------- 154: Ran 9 tests in 0.132s 154: 154: OK 156: . 156: ---------------------------------------------------------------------- 156: Ran 1 test in 0.065s 156: 156: OK 156: Testing Shape Helpers wrapper 147/235 Test #156: pyShapeHelpers ......................... Passed 0.51 sec test 159 Start 159: moldraw2DTest1 159: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 159: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D 159: Test timeout computed to be: 1500 159: ----------------- Test 1 148/235 Test #154: pyChemicalFeatures ..................... Passed 0.67 sec test 160 Start 160: moldraw2DTestCatch 160: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D 160: Test timeout computed to be: 1500 159: file test1_6.svg gave hash 1109656969U not the expected 2635907956U 159: Done 159: ----------------- Test 2 159: file test2_1.png gave hash 2906135263U not the expected 638584804U 159: file test2_2.png gave hash 1323626475U not the expected 610424244U 146: validating reference data 159: file test2_3.png gave hash 2294574389U not the expected 2179746375U 159: Done 159: ----------------- Test 4 159: file test4_1.png gave hash 2529400033U not the expected 3993974247U 159: Done 159: ----------------- Test 5 159: file test5_1.png gave hash 1609648752U not the expected 571291290U 159: file test5_2.png gave hash 2470719886U not the expected 97265124U 159: file test5_3.png gave hash 1735485981U not the expected 606188176U 159: Done 159: ----------------- Test 6 (atom labels) 159: Done 159: ----------------- Test 7 (backgrounds) 159: file test7_1.png gave hash 3442107642U not the expected 1322246680U 160: Randomness seeded to: 3614402425 160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U 160: file contourMol_2.svg gave hash 2761342533U not the expected 1815941817U 159: file test7_2.png gave hash 2446896946U not the expected 1499012715U 159: Done 159: ----------------- Test8: PrepareMolDrawing 159: Done 159: ----------------- Test multi-threaded drawing 159: reading molecules 160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U 160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U 160: file contourMol_5.svg gave hash 3376179346U not the expected 3792684719U 159: generating reference drawings 160: file testGithub3226_1.png gave hash 2884766435U not the expected 3165135374U 160: file testGithub3226_2.png gave hash 2496669020U not the expected 643975155U 160: file testGithub3226_3.png gave hash 3470350919U not the expected 3119571946U 151: 1875210760 160: file testPNGMetadata_1.png gave hash 3544974138U not the expected 997629701U 159: processing 159: launch :0 159: launch :1 159: launch :2 159: launch :3 160: file testPNGMetadata_2.png gave hash 2226910827U not the expected 1797853056U 160: [15:23:24] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [15:23:24] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-1.svg gave hash 1143910631U not the expected 2253418236U 160: [15:23:24] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [15:23:24] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-1.png gave hash 2532617830U not the expected 3894611804U 29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 158: . 158: ---------------------------------------------------------------------- 158: Ran 1 test in 0.050s 158: 158: OK 160: [15:23:24] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [15:23:24] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-2.svg gave hash 700659102U not the expected 794717511U 160: [15:23:24] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [15:23:24] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-2.png gave hash 1194644863U not the expected 1443443188U 160: [15:23:24] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [15:23:24] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-3.svg gave hash 2359787964U not the expected 3982694296U 160: [15:23:24] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [15:23:24] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-3.png gave hash 3369355742U not the expected 865629432U 160: [15:23:24] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [15:23:24] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-4.svg gave hash 1880974760U not the expected 2146113517U 160: [15:23:24] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [15:23:24] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-4.png gave hash 1247155982U not the expected 3919767093U 149/235 Test #158: pyMolCatalog ........................... Passed 0.70 sec test 161 Start 161: moldraw2DRxnTest1 161: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 161: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D 161: Test timeout computed to be: 1500 29: All 191 tests passed 29: done 29: ------------------------------------- 29: Unit tests for all MMFF constraint terms. 161: ----------------- Test 1 29: 10.0003 161: file rxn_test1_1.png gave hash 169116773U not the expected 801892091U 29: done 29: ------------------------------------- 29: Unit test for MMFF TorsionConstraint close to 0 degrees. 29: done 29: ------------------------------------- 29: Unit tests for copying MMFF ForceFields. 29: done 29: ------------------------------------- 29: Unit test for MMFF butane scan. 161: file rxn_test1_2.png gave hash 1054415001U not the expected 507435337U 148: [15:23:24] Molecule does not have explicit Hs. Consider calling AddHs() 161: file rxn_test1_3.png gave hash 1401039782U not the expected 1590809137U 161: file rxn_test1_4.png gave hash 1077411151U not the expected 1766700542U 161: file rxn_test1_5.png gave hash 1082898052U not the expected 2552100594U 161: file rxn_test1_6.png gave hash 2614641009U not the expected 3791582903U 161: file rxn_test1_7.png gave hash 2659385921U not the expected 1461397406U 161: Done 161: ----------------- Test 2: some examples that caused problems in testing 161: file rxn_test2_1.png gave hash 2159157032U not the expected 3551633840U 148: [15:23:25] Molecule does not have explicit Hs. Consider calling AddHs() 161: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>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 161: file rxn_test2_2_1.png gave hash 558529985U not the expected 1268122583U 161: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>[cH:3]1[cH:2][c:1]([cH:6][cH:5][c:4]1)Cl Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccccc4 Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccc(cc4)Cl 151: 633441040 151: =============================================================================== 151: All tests passed (73 assertions in 3 test cases) 151: 150/235 Test #151: molAlignCatchTest ...................... Passed 2.75 sec test 162 Start 162: pyMolDraw2D 162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" 162: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap 162: Test timeout computed to be: 1500 161: file rxn_test2_2_2.png gave hash 431249733U not the expected 82821108U 161: 2 Cc1c(cc([nH]1)[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)[C:7](=[O:8])[NH:9][CH2:10][CH2:11]>>CCc1nc(c(n1[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)C)[C:7](=[O:8])[NH:9][CH2:10][CH2:11] Cc1c(cc([nH]1)c2ccccc2)C(=O)NCCN3CCN(C 161: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl 161: 3 [c:1][C:2](=[O:3])[NH:4]CCC[CH2:5][N:6]([CH2:7])[CH2:8]>>[c:1][C:2](=[O:3])[NH:4]C[CH2:5][N:6]([CH2:7])[CH2:8] CCCn1c(c(cc1c2ccccc2)C(=O)NCCCCN3CCN(CC3)c4cccc(c4Cl)Cl)C CCCn1c(c(cc1c2ccccc2)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl)C 29: done 151/235 Test #29: testMMFFForceField ..................... Passed 21.05 sec test 163 Start 163: testFMCS 163: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/testFMCS 163: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS 163: Test timeout computed to be: 1500 161: file rxn_test2_2_3.png gave hash 4183177411U not the expected 3828365604U 161: 3 [CH3:1]c1c(cc(n1[CH3:2])C(C)(C)C)[C:3]>>[CH3:2]c1c(c(nc(n1)[CH3:1])[C:3])OC Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3cc(n(c3C)C)C(C)(C)C Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3c(c(nc(n3)C)C)OC 161: file rxn_test2_2_4.png gave hash 798840480U not the expected 1230108677U 161: Done 161: ----------------- Test 3: test reactant highlighting 161: file rxn_test3_1.png gave hash 4020922188U not the expected 4189980366U 161: Done 161: ----------------- Test 4: some examples from SMARTS in testing 161: draw! 148: [15:23:25] Molecule does not have explicit Hs. Consider calling AddHs() 161: file rxn_test4_1.png gave hash 1538512166U not the expected 2745201873U 161: done 161: file rxn_test4_2.png gave hash 4290002109U not the expected 3094925886U 148: [15:23:25] Molecule does not have explicit Hs. Consider calling AddHs() 161: Done 152/235 Test #161: moldraw2DRxnTest1 ...................... Passed 0.77 sec test 164 Start 164: pyFMCS 164: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Wrap/testFMCS.py" 164: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap 164: Test timeout computed to be: 1500 162: ...[15:23:25] Font file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. 162: [15:23:25] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. 162: ..........[15:23:25] 162: 162: **** 162: Pre-condition Violation 162: molecule must not be None 162: Violation occurred on line 432 in file ./Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp 162: Failed Expression: m 162: ---------- 162: Stacktrace: 162: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 162: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 162: 2# RDKit::prepMolForDrawing(RDKit::ROMol const*, bool, bool, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so 162: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector7 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so 162: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 162: 5# 0x0000FFFFADB72680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 162: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 162: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 162: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so 162: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 162: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 162: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 162: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 162: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 162: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 162: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 162: 16# 0x0000FFFFAD18B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 162: 17# 0x0000FFFFAD18B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 162: 18# 0x0000FFFFAD18B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 162: 19# 0x0000FFFFAD18B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 162: 20# 0x0000FFFFAD18B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 162: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 162: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 162: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 162: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 162: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 162: 26# 0x0000FFFFADB6F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 162: 27# _PyObject_MakeTpCall in /usr/bin/python3 162: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 29# 0x00000000005335D0 in /usr/bin/python3 162: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 31# 0x00000000004AC3B4 in /usr/bin/python3 162: 32# 0x0000000000665934 in /usr/bin/python3 162: 33# _PyObject_MakeTpCall in /usr/bin/python3 162: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 35# 0x00000000005335D0 in /usr/bin/python3 162: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 37# 0x00000000004AC3B4 in /usr/bin/python3 162: 38# 0x0000000000665934 in /usr/bin/python3 162: 39# _PyObject_MakeTpCall in /usr/bin/python3 162: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 41# 0x00000000005335D0 in /usr/bin/python3 162: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 43# 0x00000000004AC3B4 in /usr/bin/python3 162: 44# 0x0000000000665934 in /usr/bin/python3 162: 45# _PyObject_MakeTpCall in /usr/bin/python3 162: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 47# 0x0000000000505090 in /usr/bin/python3 162: 48# _PyObject_MakeTpCall in /usr/bin/python3 162: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 50# PyEval_EvalCode in /usr/bin/python3 162: 51# 0x00000000005FFD24 in /usr/bin/python3 162: 52# 0x00000000005F9904 in /usr/bin/python3 162: 53# 0x0000000000627ED4 in /usr/bin/python3 162: 54# 0x0000000000627274 in /usr/bin/python3 162: 55# 0x0000000000627010 in /usr/bin/python3 162: 56# Py_RunMain in /usr/bin/python3 162: 57# Py_BytesMain in /usr/bin/python3 162: 58# 0x0000FFFFAF49229C in /lib/aarch64-linux-gnu/libc.so.6 162: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 162: 60# _start in /usr/bin/python3 162: ---------- 162: **** 162: 148: [15:23:25] Molecule does not have explicit Hs. Consider calling AddHs() 146: processing 146: launch :0 146: launch :1 146: launch :2 146: launch :3 160: file testHandDrawn-5a.svg gave hash 2796249138U not the expected 1567781555U 160: [15:23:25] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [15:23:25] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-5b.svg gave hash 4043231252U not the expected 66354106U 160: [15:23:25] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. 160: [15:23:25] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. 162: ...................... 162: ---------------------------------------------------------------------- 162: Ran 35 tests in 0.277s 162: 162: OK 162: json lasso 160: file testHandDrawn-5.png gave hash 2430523987U not the expected 828378555U 160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U 148: [15:23:25] Molecule does not have explicit Hs. Consider calling AddHs() 160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U 153/235 Test #162: pyMolDraw2D ............................ Passed 0.85 sec test 165 Start 165: FMCStest 165: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 165: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test 165: Test timeout computed to be: 1500 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_15113.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_16613.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_30745.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_30861.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_31495.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_34869.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_36158.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_36559.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_37434.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_39147.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_43754.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_44011.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_44158.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_48076.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_48961.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_49648.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_49703.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_51128.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_51343.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_51842.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_54554.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_100_55749.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_17256.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_20244.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_20245.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_30149.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_30499.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_36186.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_39262.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_43966.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_45279.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_48029.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_49064.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_49801.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_50681.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_54039.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58265.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58358.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58866.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_60810.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_21358.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_21597.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_30111.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_30349.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_31746.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_31822.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_35220.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_37603.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_37964.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_39508.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_42164.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_42577.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_44072.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_45522.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46700.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46719.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46744.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_48517.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_49087.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_50034.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_51475.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_53483.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_53506.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_54598.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_55614.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_55737.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57090.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57705.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57785.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_58463.txt 165: 165: testChEMBfopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: L_Txt() chembl_II_sets/Target_no_10193_58700.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_61003.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_61349.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10260_38526.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10260_50778.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10260_52179.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10260_54285.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_30224.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_31222.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37349.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37369.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37465.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37541.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_38371.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_44314.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_44578.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_45765.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_46281.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_47928.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_50624.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51341.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51662.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51767.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53081.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53396.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53407.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_58823.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_59190.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_60672.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_61176.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_20905.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30074.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30175.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30423.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_31555.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_34878.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_35926.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_42168.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_20859.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_30060.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_30061.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_30606.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_30866.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_31249.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_34921.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_35188.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_36636.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_37466.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_39202.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_43952.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_49345.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_49591.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_49854.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_51416.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_53537.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_58879.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_60679.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_107_61269.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_20600.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_20859.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_30060.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_30606.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_30866.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_31558.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_35188.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_37466.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_43875.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_48911.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_49591.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_49854.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: no_108_57887.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_60679.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_108_6857.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_15478.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_20853.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30840.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30862.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30918.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30994.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31014.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31508.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31623.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35003.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35004.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35281.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35957.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_36520.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_36641.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_38586.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_44431.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_45093.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_51302.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_5247.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_52937.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_57198.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_5739.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_6535.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_20205.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_20986.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_30091.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_34698.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_34705.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37038.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37272.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37447.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_38909.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_38953.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_39472.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_45825.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_47179.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_49028.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_49860.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_51984.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_53395.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_53826.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_54121.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_54530.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_55738.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_57725.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_58590.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11365_20432.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11365_30331.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11365_37956.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11365_48114.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11365_58566.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_34731.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_34818.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37318.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37339.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37564.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_39504.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_39561.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_46082.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_46089.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_47349.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_47757.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_51593.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_54754.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_58262.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_58958.txt 165: 165: testChEMBL_Txt(fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: ) chembl_II_sets/Target_no_114_16827.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_20503.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_20724.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_30254.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_30321.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_30572.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_31116.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_31281.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_31443.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_34747.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_34920.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_35040.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_36623.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_37136.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_37208.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_38298.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_38554.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_39088.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_39543.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_44049.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_44562.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_45180.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_45867.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_46087.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_46829.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_47546.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_48395.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_50461.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_50765.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_51669.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_52381.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_57231.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_114_58246.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_30999.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_31021.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_31650.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_35011.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_37014.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_44598.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_48446.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50614.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50615.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50618.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_51950.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_31616.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_38381.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_45757.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_46816.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_50701.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_54049.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_57890.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_61045.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_30194.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_31421.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_35538.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_55727.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_60676.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_61130.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_6444.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_15623.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_20096.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_21591.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_30184.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_30380.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_30745.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_30861.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_31619.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_34869.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_35284.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_36158.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_36915.txt 165: 165: testChEMBL_Txfopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: t() chembl_II_sets/Target_no_121_37434.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_37541.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_37677.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_38837.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_39530.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_43793.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_44158.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_44164.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_44579.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_44593.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_44692.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_44914.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_45878.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_48050.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_48706.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_48944.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_48961.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_49880.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_50055.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_50512.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_51064.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_53537.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_55749.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_58879.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_121_6876.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_44664.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_46451.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_50640.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_56102.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_58015.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_59089.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_59092.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_61340.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12252_31458.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12252_38481.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12252_42104.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12252_49475.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12252_49933.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12252_50558.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_126_37249.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_126_39117.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_126_48227.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_126_48229.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_126_53969.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_126_54262.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_126_55353.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_126_61212.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20250.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20506.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20626.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20689.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_21358.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_30158.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_30349.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_34843.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_35220.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_36318.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_36800.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_39349.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_45385.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_45676.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_46700.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_46719.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_48517.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_52690.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_53483.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_55435.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_56102.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_58015.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_58375.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_1295fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: 2_58700.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_16724.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_2710.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_30128.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_31250.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_35519.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_36905.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_46788.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_4737.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_55736.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_57473.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_16146.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_30313.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_30539.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_30653.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_30988.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_31179.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_31339.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_3525.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_36886.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_37020.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_38128.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_43952.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_45210.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_45899.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_47889.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_51800.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_53158.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_5330.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_55648.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_56096.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_57287.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_57399.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_57606.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_58470.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_130_60894.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_15010.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_20304.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_20542.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_20788.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_21358.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_30349.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_31103.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_31764.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_31822.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_35220.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_37964.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_42164.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_44072.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_45522.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_46719.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_46744.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_48416.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_49740.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_50034.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_50640.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_53483.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_53506.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_53814.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_55435.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_56074.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_56107.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_57090.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_57705.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_57785.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_57861.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_58583.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_59089.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_15_59092.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_20600.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_30764.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_34876.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_37427.tfopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: xt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_38266.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_45283.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_46990.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_47123.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_47900.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_48050.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_48062.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_48076.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_50718.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_50972.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_51372.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_51830.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_53049.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_53505.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_54021.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_54565.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_54570.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_57666.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_57890.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_58072.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_58634.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_58643.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_59080.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_59202.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_59346.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_60379.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_60385.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_165_61098.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_31154.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_35648.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_48914.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_51975.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_52435.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_55790.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_58958.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_61146.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20191.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20562.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20606.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20607.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30003.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30402.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30726.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30924.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31457.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31460.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31600.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31620.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31640.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31782.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31797.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31829.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31856.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34690.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34691.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34694.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_35712.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_37497.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_37539.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48070.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48219.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48824.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48902.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_52867.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_53534.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_54570.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_58727.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_60159.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_60661.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_30037.txt 165: 165: testChEMBL_Txt() chefopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: mbl_II_sets/Target_no_259_34734.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_35365.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_35787.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_36793.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_37845.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_38328.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_39374.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_43936.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_44059.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_44405.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_44424.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_45166.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_46158.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_46425.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_47187.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_48435.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_48817.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_48849.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_48957.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_48965.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_49519.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_49921.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_50392.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_50972.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_52405.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_52442.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_53169.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_54640.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_57207.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_58537.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_58920.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_259_60358.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_25_16077.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_25_34943.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_25_36391.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_25_36574.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_25_52906.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_25_54642.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_16385.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_20333.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_20774.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_35825.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_37637.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_47741.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_48567.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_48841.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_49589.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_50564.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_51201.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_53150.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_55747.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_43_58276.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_20813.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_2331.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_2391.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_30374.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_30512.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_30796.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_31058.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_31450.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_36609.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_36636.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_38266.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_43800.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_47621.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_49433.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_49550.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_49865.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_51005.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_52373.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_53878.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_54554.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_57508.txtfopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_57618.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_59484.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_51_6563.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_61_16845.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_61_37106.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_61_37272.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_61_47947.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_61_50754.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_61_55800.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_61_57380.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_65_35328.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_65_36137.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_65_38826.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_65_44596.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_65_51275.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_65_55671.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_20155.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_30616.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_30653.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_30988.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_31339.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_31527.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_31631.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_36047.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_36568.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_36636.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_37020.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_38128.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_43952.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_45210.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_47889.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_51064.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_51800.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_5330.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_57508.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_58470.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_72_60894.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_20730.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_20753.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_30097.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_30663.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_35365.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_35375.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_35918.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_36010.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_36780.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_36793.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_37845.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_39110.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_39546.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_43936.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_44405.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_44424.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_44683.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_45166.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_46648.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_46986.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_47070.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_47187.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_48435.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_48817.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_49138.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_49460.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_49519.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_49532.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_49829.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_50608.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_54640.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_87_61082.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_90_15727.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_90_20155.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_90_30407.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_90_3525.txt 165: 165: testChEMBfopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: L_Txt() chembl_II_sets/Target_no_93_12377.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_93_1308.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_93_34759.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_93_35447.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_93_42214.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_93_45877.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_93_47082.txt 165: 165: testChEMBL_Txt() chembl_II_sets/Target_no_93_57082.txt 165: 165: testFileSDF_RandomSet(): benchmark/chembl13-10000-random-pairs.sdf 165: ERROR: RDKit could not load input file 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_pairs.smi 165: ERROR: RDKit could not load input file 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_knearest_2.smi 165: ERROR: RDKit could not load input file 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_knearest_10.smi 165: ERROR: RDKit could not load input file 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_knearest_100.smi 165: ERROR: RDKit could not load input file 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_threshold_80.smi 165: ERROR: RDKit could not load input file 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 165: ERROR: RDKit could not load input file 154/235 Test #165: FMCStest ............................... Passed 0.05 sec test 166 Start 166: molHashCatchTest 166: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest 166: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash 166: Test timeout computed to be: 1500 160: [15:23:26] unrecognized bond typefile testGithub4238_1.png gave hash 4081567765U not the expected 2623427676U 160: file testGithub4323_1.png gave hash 3210012906U not the expected 3075787867U 166: Randomness seeded to: 1678077751 166: =============================================================================== 166: All tests passed (363 assertions in 14 test cases) 166: 155/235 Test #166: molHashCatchTest ....................... Passed 0.13 sec test 167 Start 167: pyMolHash 167: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/Wrap/testMolHash.py" 167: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap 167: Test timeout computed to be: 1500 150: *********************************************************** 150: Testing O3AAlign 150: --------------------------------- 150: testMMFFO3A 150: 150: --------------------------------- 150: testMMFFO3A with pre-computed dmat and MolHistogram 150: 150: --------------------------------- 150: testMMFFO3A with constraints 150: 150: --------------------------------- 150: testMMFFO3A with variable weight constraints followed by local-only optimization 150: 150: --------------------------------- 150: testCrippenO3A 150: 150: --------------------------------- 150: testCrippenO3A with pre-computed dmat and MolHistogram 150: 150: --------------------------------- 150: testCrippenO3A with constraints 150: 150: --------------------------------- 150: testCrippenO3A with variable weight constraints followed by local-only optimization 150: 150: --------------------------------- 150: testMMFFO3A multithreading 150: 150: generating reference data 160: file testGithub4323_3.png gave hash 2585216301U not the expected 381907253U 160: [15:23:26] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. 167: .... 167: ---------------------------------------------------------------------- 167: Ran 4 tests in 0.020s 167: 167: OK 156/235 Test #167: pyMolHash .............................. Passed 0.63 sec test 168 Start 168: testMMPA 168: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/testMMPA 168: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA 168: Test timeout computed to be: 1500 163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 163: Time elapsed 0.000 seconds 163: 163: test32() 163: MCS: [#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#6]=[#6]-[#6](-[#7]-[#6]1:[#6]:[#6](-[#16](-[#7]2-[#6]-[#6]-[#8]-[#6]-[#6]-2)(=[#8])=[#8]):[#6]:[#6]:[#6]:1-[#7](-[#6]-[#6])-[#6]-[#6])=[#8] 31 atoms, 33 bonds 163: Time elapsed 0.070 seconds 163: 163: test190() 163: MCS: [#6]1:[#6]:[#6]2:[#8]:[#6](:[#7]:[#6]:2:[#6]:[#6]:1)-[#6]1:[#6]:[#6](-[#7]-[#6](=[#8])-[#6]):[#6]:[#6]:[#6]:1 19 atoms, 21 bonds 163: Time elapsed 0.009 seconds 163: 163: test3() 163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds 163: Time elapsed 0.015 seconds 163: 163: testSimpleFast() 163: MCS: [#6]-[#8]-[#6]-[#6]1:[#6]:[#7]:[#6]:[#6](:[#6]:1):[#7]:[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#8]-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#17] 24 atoms, 26 bonds 163: Time elapsed 0.088 seconds 163: 163: testSimple() 163: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds 163: Time elapsed 0.051 seconds 163: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds 163: Time elapsed 0.073 seconds 163: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds 163: Time elapsed 0.126 seconds 163: 163: testSegFault() 163: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds 163: Time elapsed 0.009 seconds 163: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds 163: Time elapsed 0.015 seconds 163: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@1 6 atoms, 6 bonds 163: Time elapsed 0.015 seconds 163: 163: testThreshold() 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: Time elapsed 0.000 seconds 163: 163: testRing1() 163: MCS: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds 163: Time elapsed 0.349 seconds 163: MCS MatchFusedRings: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds 163: Time elapsed 0.347 seconds 163: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#7;r6,!R1]:&@[#6;r6,!R1](:&@[#6]:&@[#6]:&@1)-&!@[#6](=&!@[#8])-&!@[#8]-&!@[#6](-&!@[#6])-&!@[#6] 12 atoms, 12 bonds 163: Time elapsed 0.385 seconds 163: 163: testAtomCompareIsotopes() 163: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds 163: Time elapsed 0.000 seconds 163: 163: testAtomCompareAnyAtom() 163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds 163: Time elapsed 0.000 seconds 163: 163: testAtomCompareAnyAtom() 163: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds 163: Time elapsed 0.000 seconds 163: 163: testAtomCompareAnyAtom() 163: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds 163: Time elapsed 0.000 seconds 163: 163: testAtomCompareAnyAtom() 163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds 163: Time elapsed 0.000 seconds 163: 163: testJnk1LigandsDistance() 163: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#7])-[#6]#[#7] CCOc1nc(NC(=O)Cc2ccccc2)cc(N)c1C#N 22 atoms, 23 bonds 163: Time elapsed 0.005 seconds 163: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#6,#8])-[#7])-[#6]#[#7] *c1cccc(CC(=O)Nc2cc(N)c(C#N)c(OCC)n2)c1 23 atoms, 24 bonds 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 168: Time elapsed 0.002254 seconds 168: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 168: 1: NOREF. Reference data NOT LISTED in test case. 168: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 168: 2: NOREF. Reference data NOT LISTED in test case. 168: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] 168: 3: NOREF. Reference data NOT LISTED in test case. 168: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2] 168: 4: NOREF. Reference data NOT LISTED in test case. 168: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 168: 5: NOREF. Reference data NOT LISTED in test case. 168: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 168: 6: NOREF. Reference data NOT LISTED in test case. 168: 7: res= NULL,C[C:2](C(=O)N[*:1])[NH+]1CCCC1.Cc1ccccc1[*:1] 168: 7: NOREF. Reference data NOT LISTED in test case. 168: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3] 168: 8: NOREF. Reference data NOT LISTED in test case. 168: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 168: 9: NOREF. Reference data NOT LISTED in test case. 168: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 168: 10: NOREF. Reference data NOT LISTED in test case. 168: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 168: 11: NOREF. Reference data NOT LISTED in test case. 168: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] 168: 12: NOREF. Reference data NOT LISTED in test case. 168: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2] 168: 13: NOREF. Reference data NOT LISTED in test case. 168: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 168: 14: NOREF. Reference data NOT LISTED in test case. 168: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 168: 15: NOREF. Reference data NOT LISTED in test case. 168: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] 168: 16: NOREF. Reference data NOT LISTED in test case. 168: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 168: 17: NOREF. Reference data NOT LISTED in test case. 168: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 168: 18: NOREF. Reference data NOT LISTED in test case. 148: .[15:23:26] Molecule does not have explicit Hs. Consider calling AddHs() 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 168: ----------------------------------- 168: Time elapsed 0.001954 seconds 168: 168: TEST 1 mol: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 168: 1: NULL, C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 168: 1: PASSED. matchedRefRes = 4 168: 2: O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21, C[*:1].O=C(NCCO)[*:2] 168: 2: PASSED. matchedRefRes = 1 168: 3: O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OCC[*:2] 168: 3: PASSED. matchedRefRes = 6 168: 4: O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OC[*:2] 168: 4: PASSED. matchedRefRes = 13 168: 5: O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].O[*:2] 168: 5: PASSED. matchedRefRes = 12 168: 6: NULL, Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 168: 6: PASSED. matchedRefRes = 10 168: 7: O=C(N[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 7: NOREF. Reference data NOT LISTED in test case.O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 8: O=C(NC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 8: NOREF. Reference data NOT LISTED in test case.O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 9: O=C(NCC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 9: NOREF. Reference data NOT LISTED in test case.O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 10: NULL, Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 10: PASSED. matchedRefRes = 3 168: 11: C([*:1])[*:2], Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 11: NOREF. Reference data NOT LISTED in test case.C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 12: C(C[*:2])[*:1], Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 12: PASSED. matchedRefRes = 8 168: 13: NULL, Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 13: PASSED. matchedRefRes = 9 168: 14: C([*:1])[*:2], Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 14: PASSED. matchedRefRes = 11 168: 15: NULL, Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 15: PASSED. matchedRefRes = 2 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 168: 7: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(N[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:2] 168: 14: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NCC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 15: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 168: ----------------------------------- 168: 168: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 168: Time elapsed 0.001967 seconds 168: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 168: 1: PASSED. matchedRefRes = 4 168: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] 168: 2: PASSED. matchedRefRes = 1 168: 3: res= O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OCC[*:2] 168: 3: PASSED. matchedRefRes = 6 168: 4: res= O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OC[*:2] 168: 4: PASSED. matchedRefRes = 13 168: 5: res= O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].O[*:2] 168: 5: PASSED. matchedRefRes = 12 168: 6: res= NULL,Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 168: 6: PASSED. matchedRefRes = 10 168: 7: res= O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 7: NOREF. Reference data NOT LISTED in test case. 168: 8: res= O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 8: NOREF. Reference data NOT LISTED in test case. 168: 9: res= O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 9: NOREF. Reference data NOT LISTED in test case. 168: 10: res= NULL,Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 10: PASSED. matchedRefRes = 3 168: 11: res= C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 11: NOREF. Reference data NOT LISTED in test case. 168: 12: res= C(C[*:2])[*:1],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 12: PASSED. matchedRefRes = 8 168: 13: res= NULL,Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 13: PASSED. matchedRefRes = 9 168: 14: res= C([*:1])[*:2],Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 14: PASSED. matchedRefRes = 11 168: 15: res= NULL,Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 15: PASSED. matchedRefRes = 2 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 168: 7: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(N[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:2] 168: 14: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NCC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 15: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 168: ----------------------------------- 168: 168: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE 168: Time elapsed 0.012640 seconds 168: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 168: 1: PASSED. matchedRefRes = 2 168: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] 168: 2: PASSED. matchedRefRes = 3 168: 3: res= C([*:1])([*:2])[*:3],C1CN1[*:3].C[*:1].O=C[*:2] 168: 3: NOREF. Reference data NOT LISTED in test case. 168: 4: res= C1CN1C([*:1])[*:2],C[*:1].O=C[*:2] 168: 4: PASSED. matchedRefRes = 4 168: 5: res= NULL,C1CN1[*:1].CC(C=O)[*:1] 168: 5: PASSED. matchedRefRes = 5 168: 6: res= CC([*:1])[*:2],C1CN1[*:2].O=C[*:1] 168: 6: NOREF. Reference data NOT LISTED in test case. 168: 7: res= NULL,CC(N1CC1)[*:1].O=C[*:1] 168: 7: PASSED. matchedRefRes = 7 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 1: CC(N1CC1)C(=O),Case1-SIMPLE,C([*:1])([*:2])[*:3],C1CN1[*:2].C[*:1].O=C[*:3] 168: 6: CC(N1CC1)C(=O),Case1-SIMPLE,CC([*:1])[*:2],C1CN1[*:1].O=C[*:2] 168: ----------------------------------- 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 168: Time elapsed 0.002137 seconds 168: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 168: 1: NOREF. Reference data NOT LISTED in test case. 168: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 168: 2: NOREF. Reference data NOT LISTED in test case. 168: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] 168: 3: NOREF. Reference data NOT LISTED in test case. 168: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2] 168: 4: NOREF. Reference data NOT LISTED in test case. 168: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 168: 5: NOREF. Reference data NOT LISTED in test case. 168: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 168: 6: NOREF. Reference data NOT LISTED in test case. 168: 7: res= NULL,C[C:2](C(=O)N[*:1])[NH+]1CCCC1.Cc1ccccc1[*:1] 168: 7: NOREF. Reference data NOT LISTED in test case. 168: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3] 168: 8: NOREF. Reference data NOT LISTED in test case. 168: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 168: 9: NOREF. Reference data NOT LISTED in test case. 168: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 168: 10: NOREF. Reference data NOT LISTED in test case. 168: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 168: 11: NOREF. Reference data NOT LISTED in test case. 160: file testFlexiCanvas.2a.png gave hash 2206969409U not the expected 2609920321U 168: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] 168: 12: NOREF. Reference data NOT LISTED in test case. 168: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2] 168: 13: NOREF. Reference data NOT LISTED in test case. 168: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 168: 14: NOREF. Reference data NOT LISTED in test case. 168: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 168: 15: NOREF. Reference data NOT LISTED in test case. 168: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] 168: 16: NOREF. Reference data NOT LISTED in test case. 168: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 168: 17: NOREF. Reference data NOT LISTED in test case. 168: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 168: 18: NOREF. Reference data NOT LISTED in test case. 160: file testFlexiCanvas.2b.png gave hash 2563070594U not the expected 3615599154U 163: Time elapsed 0.001 seconds 163: 163: test18() 163: Query +MAP [CH3:0][c:1]1[n:2][c:3]([CH2:4][N:5]([CH:6]([CH3:7])[c:8]2[n:9][cH:10][cH:11][cH:12][cH:13]2)[CH2:14][CH2:15][CH2:16][CH2:17][NH2:18])[cH:19][cH:20][cH:21]1 163: MCS: [#6](:[#7]:[#6]-[#6]-[#7](-[#6](-[#6])-[#6]1:[#7]:[#6]:[#6]:[#6]:[#6]:1)-[#6]-[#6]-[#6]-[#6]-[#7]):[#6]:[#6]:[#6] 21 atoms, 21 bonds 163: Time elapsed 0.008 seconds 163: 163: test504() 163: Query +MAP [CH2:0]([CH2:1][CH2:2][NH:3][C:4]([CH:5]1[CH2:6][CH:7]1[c:8]1[c:9][c:10]([Cl:11])[c:12]([Cl:13])[cH:14][c:15]1)=[O:16])[CH2:17][CH2:18][N:19]1[CH2:20][CH2:21][CH:22]([NH:23][C:24]([NH:25][c:26]2[cH:27][cH:28][c:29]([Cl:30])[cH:31][cH:32]2)=[O:33])[CH2:34]1 163: MCS: [#6](-[#6]-[#6]-[#7]-[#6](-[#6]1-[#6]-[#6]-1-[#6]1:[#6]:[#6](-[#17]):[#6](:[#6]:[#6]:1)-[#17])=[#8])-[#6]-[#6]-[#7](-[#6]-[#6]-[#6]-[#7]-[#6](-[#7]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)=[#8])-[#6] 34 atoms, 36 bonds 163: Time elapsed 0.102 seconds 163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 163: Time elapsed 0.001 seconds 163: MCS: [#6]1-[#6]-[#7]-[#6](-[#6]-[#7]-1-[#6]1:[#6](:[#6]:[#6]2:[#6](:[#6](:[#6]:[#7](-[#6]3-[#6]-[#6]-3):[#6]:2:[#6]:1)-[#6](=[#8])-[#8])=[#8])-[#9])-[#6] 25 atoms, 28 bonds 163: Time elapsed 0.030 seconds 163: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds 163: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0009 seconds. bond[0]=6 163: STATISTICS: 163: Total Growing Steps = 1, MCS found on 1 step, for 0.0009 seconds 163: Initial Seeds = 1, Mismatched 0 163: Inspected Seeds = 2 163: Rejected by BestSize = 0 163: IndividualBondExcluded = 0 163: MatchCheck Seeds = 2 163: MatchCalls = 2 163: MatchFound = 1 163: fastMatchCalls = 1 163: fastMatchFound = 0 163: slowMatchCalls = 2 163: slowMatchFound = 1 163: DupCacheFound = 0 0 matched, 0 mismatched 163: HashCache size = 1 keys 163: HashCache size = 1 entries 163: FindHashInCache = 2 163: HashFoundInCache= 0 163: ExactMatchCalls = 0 163: ExactMatchFound = 0 163: Time elapsed 0.001 seconds 163: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 163: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 163: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 163: res sub = 1 size=3 163: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds 163: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 163: res sub = 1 size=3 163: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds 163: test target = CC[C@H](F)Cl query = CCC useChirality = 0 163: res sub = 1 size=3 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: test target = CC[C@H](F)Cl query = CCC useChirality = 1 163: res sub = 1 size=3 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: test target = CCC(F)Cl query = CC useChirality = 0 163: res sub = 1 size=2 163: MCS: [#6]-[#6] 2 atoms, 1 bonds 163: test target = CCC(F)Cl query = CC useChirality = 1 163: res sub = 1 size=2 163: MCS: [#6]-[#6] 2 atoms, 1 bonds 163: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 163: res sub = 1 size=4 163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 163: res sub = 1 size=4 163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 163: res sub = 1 size=4 163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 163: res sub = 1 size=4 163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 163: res sub = 0 size=0 163: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds 163: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 163: res sub = 0 size=0 163: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds 163: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 163: res sub = 1 size=4 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 168: ----------------------------------- 168: 168: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 168: Time elapsed 0.010509 seconds 168: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1 168: 1: NOREF. Reference data NOT LISTED in test case. 168: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 168: 2: NOREF. Reference data NOT LISTED in test case. 168: 3: res= O=C(O[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc(C[*:2])cc1 168: 3: NOREF. Reference data NOT LISTED in test case. 168: 4: res= O=C(O[*:1])C(c1ccccc1)[*:2],O[*:2].c1ccc(C[*:1])cc1 168: 4: NOREF. Reference data NOT LISTED in test case. 168: 5: res= O=C(O[*:1])C([*:2])[*:3],O[*:2].c1ccc(C[*:1])cc1.c1ccc([*:3])cc1 168: 5: NOREF. Reference data NOT LISTED in test case. 168: 6: res= O=C(O[*:1])C(O)[*:2],c1ccc(C[*:1])cc1.c1ccc([*:2])cc1 168: 6: NOREF. Reference data NOT LISTED in test case. 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 163: res sub = 1 size=4 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 163: res sub = 1 size=4 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 163: res sub = 1 size=4 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 163: res sub = 1 size=4 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 163: res sub = 0 size=0 163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 163: test target = OC(F)CCl query = OC(F)C useChirality = 0 163: res sub = 1 size=4 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = OC(F)CCl query = OC(F)C useChirality = 1 163: res sub = 1 size=4 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 163: res sub = 1 size=4 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 163: res sub = 0 size=0 163: MCS: [#9] 1 atoms, 0 bonds 163: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 163: res sub = 1 size=4 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 163: res sub = 0 size=0 163: MCS: [#9] 1 atoms, 0 bonds 163: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 163: res sub = 1 size=3 163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 163: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 163: res sub = 1 size=3 163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 163: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 163: res sub = 1 size=3 163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 163: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 163: res sub = 1 size=3 163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 163: 163: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> 163: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 163: res sub = 1 size=3 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 163: res sub = 1 size=3 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: done 168: 7: res= NULL,O=C(OC[*:1])C(O)c1ccccc1.c1ccc([*:1])cc1 168: 7: NOREF. Reference data NOT LISTED in test case. 168: 8: res= O=C(OC[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc([*:2])cc1 168: 8: NOREF. Reference data NOT LISTED in test case. 168: 9: res= O=C(OC[*:2])C(c1ccccc1)[*:1],O[*:1].c1ccc([*:2])cc1 168: 9: NOREF. Reference data NOT LISTED in test case. 168: 10: res= O=C(OC[*:2])C([*:1])[*:3],O[*:1].c1ccc([*:2])cc1.c1ccc([*:3])cc1 168: 10: NOREF. Reference data NOT LISTED in test case. 168: 11: res= O=C(OC[*:1])C(O)[*:2],c1ccc([*:1])cc1.c1ccc([*:2])cc1 168: 11: NOREF. Reference data NOT LISTED in test case. 168: 12: res= NULL,O=C(OCc1ccccc1)[*:1].OC(c1ccccc1)[*:1] 168: 12: NOREF. Reference data NOT LISTED in test case. 168: 13: res= c1ccc(C([*:1])[*:2])cc1,O=C(OCc1ccccc1)[*:1].O[*:2] 168: 13: NOREF. Reference data NOT LISTED in test case. 168: 14: res= C([*:1])([*:2])[*:3],O=C(OCc1ccccc1)[*:1].O[*:2].c1ccc([*:3])cc1 168: 14: PASSED. matchedRefRes = 1 168: 15: res= OC([*:1])[*:2],O=C(OCc1ccccc1)[*:1].c1ccc([*:2])cc1 168: 15: NOREF. Reference data NOT LISTED in test case. 168: 16: res= NULL,O=C(OCc1ccccc1)C(c1ccccc1)[*:1].O[*:1] 168: 16: NOREF. Reference data NOT LISTED in test case. 168: 17: res= O=C(OCc1ccccc1)C([*:1])[*:2],O[*:1].c1ccc([*:2])cc1 168: 17: NOREF. Reference data NOT LISTED in test case. 168: 18: res= NULL,O=C(OCc1ccccc1)C(O)[*:1].c1ccc([*:1])cc1 168: 18: NOREF. Reference data NOT LISTED in test case. 168: 168: --- ALL PASSED --- 168: ----------------------------------- 168: 5 TEST CASES FAILED 157/235 Test #168: testMMPA ............................... Passed 0.24 sec test 169 Start 169: pyMMPA 169: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/Wrap/testMMPA.py" 169: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap 169: Test timeout computed to be: 1500 160: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U 160: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U 160: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U 160: file testGithub4764.sz1.png gave hash 434772931U not the expected 2179222277U 160: file testGithub4764.sz2.png gave hash 3567858909U not the expected 444262090U 160: file testGithub4764.sz3.png gave hash 3541535490U not the expected 3567162200U 160: file github5383_1.svg gave hash 2761342533U not the expected 1815941817U 160: file github5383_2.svg gave hash 2560846108U not the expected 0U 160: file github5383_1.png gave hash 186818321U not the expected 2893520928U 160: file acs1996_1.png gave hash 1116230394U not the expected 2329725800U 160: file acs1996_2.png gave hash 910959002U not the expected 2996350718U 160: file acs1996_3.svg gave hash 510450189U not the expected 879041204U 160: file acs1996_8.svg gave hash 3359655656U not the expected 4110469272U 160: file acs1996_10.svg gave hash 1008047306U not the expected 2229333301U 160: [15:23:27] ACS drawing mode works best with a flexiCanvas i.e. a drawer created with width and height of -1. The scale will be fixed, and that may not look great with a pre-determined size. 160: file bond_highlights_8.svg gave hash 197391689U not the expected 3119784980U 160: file test_github5947.svg gave hash 737562322U not the expected 3122633523U 150: processing 150: launch :0 150: launch :1 150: launch :2 150: launch :3 160: file test_github6112.svg gave hash 3291975047U not the expected 3278777629U 160: file github6336_1.png gave hash 1930712448U not the expected 2958833204U 160: file AtropManyChiralsEnhanced.svg gave hash 643650995U not the expected 2256768013U 160: file testWedgingShouldBeOnSingleBond.svg gave hash 2637422009U not the expected 1002741488U 160: file testHighlightHeteroAtoms_1.svg gave hash 4006401146U not the expected 1769258632U 160: file testHighlightHeteroAtoms_2.svg gave hash 1248188292U not the expected 893937335U 160: file testGithub_7739_1.svg gave hash 1295207536U not the expected 2615562225U 160: file testGithub_7739_3.svg gave hash 3850267352U not the expected 1037942338U 160: file testGithub_7739_4.svg gave hash 1411616678U not the expected 3549083171U 160: [15:23:28] 160: 160: **** 160: Pre-condition Violation 160: 160: Violation occurred on line 206 in file ./Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp 160: Failed Expression: atomIdx < atCds_.size() && atomIdx < atomLabels_.size() 160: ---------- 160: Stacktrace: 160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 160: 2# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::calcSymbolEllipse(unsigned int, RDGeom::Point2D&, double&, double&) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeAtomHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 8# 0x0000AAAAE5965780 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 9# 0x0000AAAAE5A3514C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 10# 0x0000AAAAE5A35B00 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 11# 0x0000AAAAE5A35F34 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 12# 0x0000AAAAE5A0A7F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 13# 0x0000AAAAE5A0AD44 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 14# 0x0000AAAAE595EA70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 15# 0x0000FFFF9F38229C in /lib/aarch64-linux-gnu/libc.so.6 160: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 160: 17# 0x0000AAAAE595EB30 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: ---------- 160: **** 160: 160: [15:23:28] 160: 160: **** 160: Range Error 160: idx 160: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp 160: Failed Expression: 2 < 0 160: ---------- 160: Stacktrace: 160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 160: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 160: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 8# 0x0000AAAAE59651C4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 9# 0x0000AAAAE5A3514C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 10# 0x0000AAAAE5A35B00 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 11# 0x0000AAAAE5A35F34 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 12# 0x0000AAAAE5A0A7F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 13# 0x0000AAAAE5A0AD44 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 14# 0x0000AAAAE595EA70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 15# 0x0000FFFF9F38229C in /lib/aarch64-linux-gnu/libc.so.6 160: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 160: 17# 0x0000AAAAE595EB30 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: ---------- 160: **** 160: 160: [15:23:28] 160: 160: **** 160: Range Error 160: idx 160: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp 160: Failed Expression: 0 < 0 160: ---------- 160: Stacktrace: 160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 160: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 160: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 8# 0x0000AAAAE596582C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 9# 0x0000AAAAE5A3514C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 10# 0x0000AAAAE5A35B00 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 11# 0x0000AAAAE5A35F34 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 12# 0x0000AAAAE5A0A7F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 13# 0x0000AAAAE5A0AD44 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 14# 0x0000AAAAE595EA70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: 15# 0x0000FFFF9F38229C in /lib/aarch64-linux-gnu/libc.so.6 160: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 160: 17# 0x0000AAAAE595EB30 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: ---------- 160: **** 160: 160: file testSmallReactionCanvas.svg gave hash 3859901121U not the expected 2238356155U 163: [15:23:28] The provided InitialSeed is not an MCS and will be ignored 160: =============================================================================== 160: All tests passed (6853 assertions in 115 test cases) 160: 158/235 Test #160: moldraw2DTestCatch ..................... Passed 4.45 sec test 170 Start 170: testRascalMCES 170: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES 170: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES 170: Test timeout computed to be: 1500 169: ......... 169: ---------------------------------------------------------------------- 169: Ran 9 tests in 2.908s 169: 169: OK 159/235 Test #169: pyMMPA ................................. Passed 3.54 sec test 171 Start 171: testRascalCluster 171: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster 171: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES 171: Test timeout computed to be: 1500 164: ........................................[15:23:30] The provided InitialSeed is not an MCS and will be ignored 164: [15:23:30] The provided InitialSeed is not an MCS and will be ignored 164: [15:23:30] The provided InitialSeed is not an MCS and will be ignored 164: .[15:23:30] The provided InitialSeed is not an MCS and will be ignored 164: [15:23:30] The provided InitialSeed is not an MCS and will be ignored 164: [15:23:30] The provided InitialSeed is not an MCS and will be ignored 164: .[15:23:30] The provided InitialSeed is not an MCS and will be ignored 164: [15:23:30] The provided InitialSeed is not an MCS and will be ignored 164: [15:23:30] The provided InitialSeed is not an MCS and will be ignored 164: .[15:23:30] The provided InitialSeed is not an MCS and will be ignored 164: [15:23:30] The provided InitialSeed is not an MCS and will be ignored 164: [15:23:30] The provided InitialSeed is not an MCS and will be ignored 164: ................. 164: ---------------------------------------------------------------------- 164: Ran 60 tests in 5.227s 164: 164: OK 160/235 Test #164: pyFMCS ................................. Passed 5.79 sec test 172 Start 172: pyRascalMCES 172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" 172: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap 172: Test timeout computed to be: 1500 159: Done 159: ----------------- Test Github #781: Rendering single-atom molecules 159: Done 159: ----------------- Test 3 159: file test3_1.png gave hash 1181396669U not the expected 675908852U 159: file test3_2.png gave hash 4048792454U not the expected 2452584093U 159: file test3_3.png gave hash 2988441799U not the expected 1907006999U 159: file test3_3.svg gave hash 1119144208U not the expected 1375178959U 159: file test3_4.png gave hash 219478152U not the expected 2305641511U 159: file test3_4.svg gave hash 2680534430U not the expected 187720898U 159: file test3_5.png gave hash 2409343939U not the expected 3842605920U 159: file test3_5.svg gave hash 3625812711U not the expected 300865579U 159: file test3_6.png gave hash 1038404642U not the expected 662622011U 159: file test3_7.png gave hash 1048229413U not the expected 469729412U 159: Done 159: ----------------- Test Github774: upside-down drawings 159: file test774_1.png gave hash 2642778207U not the expected 428322245U 159: file test774_2.png gave hash 3956536315U not the expected 4095288521U 159: Done 159: ----------------- Test 9 (molecule legends) 159: file test9_1.svg gave hash 923579170U not the expected 1484349178U 159: Done 159: ----------------- Test Github852: Lines used to wedge bonds are too thick 159: file test852_1.png gave hash 2380819510U not the expected 271517011U 159: file test852_2.png gave hash 2055763177U not the expected 967452082U 159: ---------------- 159: ---------------- 159: ---------------- 159: ---------------- 159: Done 159: ----------------- Test Github860: Atom symbols in wrong order if bond comes from right 159: file test860_1.png gave hash 257586724U not the expected 2835587240U 159: file test860_2.png gave hash 2456030180U not the expected 1116015475U 159: file test860_3.png gave hash 1098011815U not the expected 1872467868U 159: Done 159: ----------------- Test Github #910: ugly coordinates generated for peptide chains 159: Done 159: ----------------- Test Github #932: mistake in SVG for wedged bonds 159: Done 159: ----------------- Test Github #953: default color should not be cyan 159: Done 159: ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly 159: Done 159: ----------------- Test Deuterium, Tritium 159: Done 159: ----------------- Test crossed bonds 159: Done 159: ----------------- Testing drawing a second molecule 159: Done 159: ----------------- Testing drawing a grid of molecules 159: Done 159: ----------------- Testing drawMolecules 159: file test12_1.svg gave hash 76786371U not the expected 826649652U 172: ..........[15:23:32] Too many matching bond pairs (1032) so can't continue. 159: Done 159: ----------------- Test JSON Configuration 159: Done 159: ----------------- Testing github 1090: escape html characters in SVG output 159: Done 159: ----------------- Testing github 1035: overflow bug in SVG color generation 159: Done 159: ----------------- Testing github 1271: MolDraw2D not drawing anything for molecules aligned with the X or Y axes 159: Done 159: ----------------- Testing github 1322: add custom atom labels 159: Done 159: ----------------- Testing use of a black & white palette 159: Done 159: ----------------- Testing use of continuous highlighting with drawMolecules 159: Done 159: ----------------- Test 17 - Testing maximum font size 159: Done 159: ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list 159: Done 159: ----------------- Testing use of fixed scales for drawing. 159: Done 159: ----------------- Testing rotation of 2D drawing. 159: Done 159: ----------------- Testing inclusion of molecule metadata 159: Done 159: ----------------- Testing Github2063: Drawing racemic bond stereo as crossed bonds should be the default 159: Done 159: ----------------- Testing Github2151: MolDraw2D: line width should be controlled by MolDrawOptions 159: file testGithub2151_1.svg gave hash 255849476U not the expected 4119581143U 159: file testGithub2151_2.svg gave hash 1195866900U not the expected 425960913U 159: Done 159: ----------------- Testing testGithub2762: MolDraw2D: HCl and ethane should be drawn 159: Done 159: ----------------- Testing testGithub2931: multi-coloured molecule highlights. 159: file testGithub2931_1.svg gave hash 608211058U not the expected 3635831631U 159: file testGithub2931_3.svg gave hash 1702246706U not the expected 2885834646U 159: Done 159: ----------------- Testing annotation of 2D Drawing. 159: file test20_1.png gave hash 603582571U not the expected 200877868U 159: file test20_2.png gave hash 1242566434U not the expected 1651164846U 159: file test20_3.png gave hash 2691880468U not the expected 1463603076U 159: file test20_4.png gave hash 1109699693U not the expected 1714613205U 159: Done 159: ----------------- Test 21 - different font 159: Done 159: ----------------- Test 22 - draw explicit methyls. 159: Done 159: ----------------- Testing drawing of legends. 159: Done 159: ----------------- Test Github 3305 - change and scale line widths. 159: file testGithub3305_1.png gave hash 4150888292U not the expected 3303791649U 159: file testGithub3305_2.png gave hash 646602948U not the expected 4003267433U 159: file testGithub3305_3.png gave hash 1486625920U not the expected 273338209U 159: file testGithub3305_4.png gave hash 2409343939U not the expected 3842605920U 159: file testGithub3305_4.svg gave hash 3625812711U not the expected 300865579U 159: file testGithub3305_5.png gave hash 1913144252U not the expected 151279576U 159: file testGithub3305_5.svg gave hash 3310590632U not the expected 1335449325U 159: file testGithub3305_6.png gave hash 1919875297U not the expected 613418460U 159: file testGithub3305_7.png gave hash 3442727171U not the expected 2835747678U 159: Done 159: ----------------- Test Github 3391 - maxFontSize interacting badly with DrawMolecules. 159: Done 159: ----------------- Test Github 4156 - bad scale for radicals in grid 159: Done 159: ----------------- Test JSON atomColourPalette 159: Done 159: ----------------- Test draw aromatic OR queries 159: Done 159: ----------------- Test AND queries 159: Done 161/235 Test #159: moldraw2DTest1 ......................... Passed 8.98 sec test 173 Start 173: testSynthonSpaceSubstructureSearch 173: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch 173: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch 173: Test timeout computed to be: 1500 172: .... 172: ---------------------------------------------------------------------- 172: Ran 14 tests in 2.663s 172: 172: OK 162/235 Test #172: pyRascalMCES ........................... Passed 3.42 sec test 174 Start 174: testCIPLabeler 174: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler 174: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler 174: Test timeout computed to be: 1500 173: Randomness seeded to: 2728322522 173: [15:23:34] Writing the enumerated file may take quite some time and result in a large file. 174: Randomness seeded to: 4074356387 174: [15:23:34] non kekulizable aromatic bond being treated as bond order 1 174: [15:23:34] non kekulizable aromatic bond being treated as bond order 1 174: [15:23:34] non kekulizable aromatic bond being treated as bond order 1 174: [15:23:34] non kekulizable aromatic bond being treated as bond order 1 174: [15:23:34] non kekulizable aromatic bond being treated as bond order 1 174: [15:23:34] non kekulizable aromatic bond being treated as bond order 1 174: [15:23:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 174: [15:23:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 174: =============================================================================== 174: All tests passed (6577 assertions in 19 test cases) 174: 163/235 Test #174: testCIPLabeler ......................... Passed 0.36 sec test 175 Start 175: pyCIPLabelsWrapTest 175: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" 175: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 175: Test timeout computed to be: 1500 175: .... 175: ---------------------------------------------------------------------- 175: Ran 4 tests in 0.052s 175: 175: OK 164/235 Test #175: pyCIPLabelsWrapTest .................... Passed 0.81 sec test 176 Start 176: pyCIPLabelsValidation 176: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" 176: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 176: Test timeout computed to be: 1500 152: .............[15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() 152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() 152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() 152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() 152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() 152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() 152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() 152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() 152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() 152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() 152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() 171: Randomness seeded to: 570871552 171: /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/data/chembl_1907596.smi 170: Randomness seeded to: 1355402787 170: [15:23:39] Timed out after 11 seconds. 173: [15:23:40] Building the fingerprints may take some time. 152: ...[15:23:41] Molecule does not have explicit Hs. Consider calling AddHs() 152: [15:23:41] Molecule does not have explicit Hs. Consider calling AddHs() 152: [15:23:41] Molecule does not have explicit Hs. Consider calling AddHs() 152: [15:23:41] Molecule does not have explicit Hs. Consider calling AddHs() 152: [15:23:41] Molecule does not have explicit Hs. Consider calling AddHs() 152: ... 152: ---------------------------------------------------------------------- 152: Ran 19 tests in 17.678s 152: 152: OK 152: Testing MolAlign Wrappers 165/235 Test #152: pyMolAlign ............................. Passed 18.28 sec test 177 Start 177: deprotectTest 177: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/deprotectTest 177: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect 177: Test timeout computed to be: 1500 177: Randomness seeded to: 1799758318 177: =============================================================================== 177: All tests passed (111 assertions in 3 test cases) 177: 166/235 Test #177: deprotectTest .......................... Passed 0.22 sec test 178 Start 178: pyDeprotect 178: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect/Wrap/rough_test.py" 178: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/Wrap 178: Test timeout computed to be: 1500 178: ..... 178: ---------------------------------------------------------------------- 178: Ran 5 tests in 0.163s 178: 178: OK 178: Testing tert-butyldimethylsilyl 178: Testing methoxytrityl 178: Testing tetrahydropyranyl 178: Testing methoxymethyl_ether 178: Testing beta-Methoxyethoxymethyl_ether 178: Testing benzyl 178: Testing trimethylsilyl 178: Testing benzoyl 178: Testing pivaloyl 178: Testing triisopropylsilyl 178: Testing acetyl 178: Testing para-methoxybenzyl_ether 178: Testing triphenylmethyl 178: Testing phthaloyl 178: Testing trimethylsilylethoxymethyl 178: Testing para-methoxyphenyl 178: Testing tosyl 178: Testing tert-butyloxycarbonyl 178: Testing trifluoroacetyl 178: Testing benzoyl 178: Testing 9-fluorenylmethyloxycarbonyl 178: Testing benzylamine 178: Testing acetamide 178: Testing carbobenzyloxy 178: Testing Acetal/Ketal 178: Testing tert-butyldimethylsilyl 178: Testing methoxytrityl 178: Testing tetrahydropyranyl 178: Testing methoxymethyl_ether 178: Testing beta-Methoxyethoxymethyl_ether 178: Testing benzyl 178: Testing trimethylsilyl 178: Testing benzoyl 178: Testing pivaloyl 178: Testing triisopropylsilyl 178: Testing acetyl 178: Testing para-methoxybenzyl_ether 178: Testing triphenylmethyl 178: Testing phthaloyl 178: Testing trimethylsilylethoxymethyl 178: Testing para-methoxyphenyl 178: Testing tosyl 178: Testing tert-butyloxycarbonyl 178: Testing trifluoroacetyl 178: Testing benzoyl 178: Testing 9-fluorenylmethyloxycarbonyl 178: Testing benzylamine 178: Testing acetamide 178: Testing carbobenzyloxy 178: Testing Acetal/Ketal 167/235 Test #178: pyDeprotect ............................ Passed 1.94 sec test 179 Start 179: testReducedGraphs 179: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs 179: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs 179: Test timeout computed to be: 1500 179: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 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, ] 179: 168/235 Test #179: testReducedGraphs ...................... Passed 0.17 sec test 180 Start 180: pyReducedGraphs 180: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" 180: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap 180: Test timeout computed to be: 1500 180: ..... 180: ---------------------------------------------------------------------- 180: Ran 5 tests in 0.059s 180: 180: OK 169/235 Test #180: pyReducedGraphs ........................ Passed 1.77 sec test 181 Start 181: trajectoryTest 181: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest 181: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory 181: Test timeout computed to be: 1500 170/235 Test #181: trajectoryTest ......................... Passed 1.02 sec test 182 Start 182: substructLibraryTest 182: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest 182: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary 182: Test timeout computed to be: 1500 182: [15:23:46] ------------------------------------- 182: [15:23:46] Test1 182: [15:23:47] done 182: [15:23:47] ------------------------------------- 182: [15:23:47] Test2 182: [15:23:47] done 182: [15:23:47] ------------------------------------- 182: [15:23:47] Test3 (stereo options) 182: [15:23:48] Done (stereo options) 182: [15:23:48] ------------------------------------- 182: [15:23:48] Test4 (trusted smiles) 182: [15:23:48] Done (trusted smiles) 182: [15:23:48] ------------------------------------- 182: [15:23:48] Testing C++ docs 182: [15:23:48] Done (C++ doc tests) 182: [15:23:48] ------------------------------------- 182: [15:23:48] Testing C++ ring query: PatternHolder 182: [15:23:48] Done (C++ ring query tests) 182: [15:23:48] ------------------------------------- 182: [15:23:48] Testing C++ ring query: TautomerPatternHolder 182: [15:23:48] Done (C++ ring query tests) 182: [15:23:48] ------------------------------------- 182: [15:23:48] Add Patterns 176: VS001: PASSED 176: VS002: PASSED 176: VS003: PASSED 176: VS004: PASSED 176: VS005: PASSED 176: VS006: PASSED 176: VS007: PASSED 176: VS008: PASSED 176: VS009: PASSED 176: VS010: PASSED 176: VS011: PASSED 176: VS012: PASSED 176: VS013: PASSED 176: VS014: PASSED 176: VS015: PASSED 176: VS016: PASSED 176: VS017: PASSED 176: VS018: PASSED 176: VS019: PASSED 176: VS020: PASSED 176: VS021: PASSED 176: VS022: PASSED 176: VS023: PASSED 176: VS024: PASSED 176: VS025: PASSED 176: VS026: PASSED 176: VS027: PASSED 176: VS028: PASSED 176: VS029: PASSED 176: VS030: PASSED 176: VS031: PASSED 176: VS032: PASSED 176: VS033: PASSED 176: VS034: PASSED 176: VS035: PASSED 176: VS036: PASSED 176: VS037: PASSED 176: VS038: PASSED 176: VS039: PASSED 176: VS040: PASSED 176: VS041: PASSED 176: VS042: PASSED 176: VS043: PASSED 176: VS044: PASSED 176: VS045: PASSED 176: VS046: PASSED 176: VS047: PASSED 176: VS048: PASSED 176: VS049: PASSED 176: VS050: PASSED 176: VS051: PASSED 176: VS052: PASSED 176: VS053: PASSED 176: VS054: PASSED 176: VS055: PASSED 176: VS056: PASSED 176: VS057: PASSED 176: VS058: PASSED 176: VS059: PASSED 176: VS060: PASSED 176: VS061: PASSED 176: VS062: PASSED 176: VS063: PASSED 176: VS064: PASSED 176: VS065: PASSED 176: VS066: PASSED 176: VS067: PASSED 176: VS068: PASSED 176: VS069: PASSED 176: VS070: PASSED 176: VS071: PASSED 176: VS072: PASSED 176: VS073: PASSED 176: VS074: PASSED 176: VS075: PASSED 176: VS076: PASSED 176: VS077: PASSED 176: VS078: PASSED 176: VS079: PASSED 176: VS080: PASSED 176: VS081: PASSED 176: VS082: PASSED 176: VS083: PASSED 176: VS084: PASSED 176: VS085: PASSED 176: VS086: PASSED 176: VS087: PASSED 176: VS088: PASSED 176: VS089: PASSED 176: VS090: PASSED 176: VS091: PASSED 176: VS092: PASSED 176: VS093: PASSED 176: VS094: PASSED 176: VS095: PASSED 176: VS096: PASSED 176: VS097: PASSED 176: VS098: PASSED 176: VS099: PASSED 176: VS100: PASSED 176: VS101: PASSED 176: VS102: PASSED 176: VS103: PASSED 176: VS104: PASSED 176: VS105: PASSED 176: VS106: PASSED 176: VS107: PASSED 176: VS108: PASSED 176: VS109: PASSED 176: VS110: PASSED 176: VS111: PASSED 176: VS112: PASSED 176: VS113: PASSED 176: VS114: PASSED 176: VS115: PASSED 176: VS116: PASSED 176: VS117: PASSED 176: VS118: PASSED 176: VS119: PASSED 176: VS120: PASSED 176: VS121: PASSED 176: VS122: PASSED 176: VS123: PASSED 176: VS124: PASSED 176: VS125: PASSED 176: VS126: PASSED 176: VS127: PASSED 176: VS128: PASSED 176: VS129: PASSED 176: VS130: PASSED 176: VS131: PASSED 176: VS132: PASSED 176: VS133: PASSED 176: VS134: PASSED 176: VS135: PASSED 176: VS136: PASSED 176: VS137: PASSED 176: VS138: PASSED 176: VS139: PASSED 176: VS140: PASSED 176: VS141: PASSED 176: VS142: PASSED 176: VS143: PASSED 176: VS144: PASSED 176: VS145: PASSED 176: VS146: PASSED 176: VS147: PASSED 176: VS148: PASSED 176: VS149: PASSED 176: VS150: PASSED 176: VS151: PASSED 176: VS152: PASSED 176: VS153: PASSED 176: VS154: PASSED 176: VS155: PASSED 176: VS156: PASSED 176: VS157: PASSED 176: VS158: PASSED 176: VS159: PASSED 176: VS160: PASSED 176: VS161: PASSED 176: VS162: PASSED 176: VS163: PASSED 176: VS164: PASSED 176: VS165: PASSED 176: VS166: PASSED 176: VS167: PASSED 176: VS168: PASSED 176: VS169: PASSED 176: VS170: PASSED 176: VS171: PASSED 176: VS172: PASSED 176: VS173: PASSED 176: VS174: PASSED 176: VS175: PASSED 176: VS176: PASSED 176: VS177: PASSED 176: VS178: PASSED 176: VS179: PASSED 176: VS180: PASSED 176: VS181: PASSED 176: VS182: PASSED 176: VS183: PASSED 176: VS184: PASSED 176: VS185: PASSED 176: VS186: PASSED 176: VS187: PASSED 176: VS188: PASSED 176: VS189: PASSED 176: VS190: PASSED 176: VS191: PASSED 176: VS192: PASSED 176: VS193: PASSED 176: VS194: PASSED 176: VS195: PASSED 176: VS196: PASSED 176: VS197: PASSED 176: VS198: PASSED 176: VS199: PASSED 176: VS200: PASSED 176: VS201: PASSED 176: VS202: PASSED 176: VS203: PASSED 176: VS204: PASSED 176: VS205: PASSED 176: VS206: PASSED 176: VS207: PASSED 176: VS208: PASSED 176: VS209: PASSED 176: VS210: PASSED 176: VS211: PASSED 176: VS212: PASSED 176: VS213: PASSED 176: VS214: PASSED 176: VS215: PASSED 176: VS216: PASSED 176: VS217: PASSED 176: VS218: PASSED 176: VS219: PASSED 176: VS220: PASSED 176: VS221: PASSED 176: VS222: PASSED 176: VS223: PASSED 176: VS224: PASSED 176: VS225: PASSED 176: VS226: PASSED 176: VS227: PASSED 176: VS228: PASSED 176: VS229: PASSED 176: VS230: PASSED 176: VS231: PASSED 176: VS232: PASSED 176: VS233: PASSED 176: VS234: PASSED 176: VS235: PASSED 176: VS236: PASSED 176: VS237: PASSED 176: VS238: PASSED 176: VS239: PASSED 176: VS240: PASSED 176: VS241: PASSED 176: VS242: PASSED 176: VS243: PASSED 176: VS244: PASSED 176: VS245: PASSED 176: VS246: PASSED 176: VS247: PASSED 176: VS248: PASSED 176: VS249: PASSED 176: VS250: PASSED 176: VS251: PASSED 176: VS252: PASSED 176: VS253: PASSED 176: VS254: PASSED 176: VS255: PASSED 176: VS256: PASSED 176: VS257: PASSED 176: VS258: PASSED 176: VS259: PASSED 176: VS260: PASSED 176: VS261: PASSED 176: VS262: PASSED 176: VS263: PASSED 176: VS264: PASSED 176: VS265: PASSED 176: VS266: PASSED 176: VS267: PASSED 176: VS268: PASSED 176: VS269: PASSED 176: VS270: PASSED 176: VS271: PASSED 176: VS272: PASSED 176: VS273: PASSED 176: VS274: PASSED 176: VS275: PASSED 176: VS276: PASSED 176: VS277: PASSED 176: VS278: PASSED 176: VS279: PASSED 176: VS280: PASSED 176: VS281: PASSED 176: VS282: PASSED 176: VS283: PASSED 176: VS284: PASSED 176: VS285: PASSED 176: VS286: PASSED 176: VS287: PASSED 176: VS288: PASSED 176: VS289: PASSED 176: VS290: PASSED 176: VS291: PASSED 176: VS292: PASSED 176: VS293: PASSED 176: VS294: PASSED 176: VS295: PASSED 176: VS296: PASSED 176: VS297: PASSED 176: VS298: PASSED 176: VS299: PASSED 176: VS300: PASSED 176: Check finished: 0 molecules failed. 176: Failed: 171/235 Test #176: pyCIPLabelsValidation .................. Passed 15.53 sec test 183 Start 183: substructLibraryCatchTest 183: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest 183: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary 183: Test timeout computed to be: 1500 183: Randomness seeded to: 112852166 183: =============================================================================== 183: All tests passed (171 assertions in 5 test cases) 183: 172/235 Test #183: substructLibraryCatchTest .............. Passed 1.79 sec test 184 Start 184: pySubstructLibrary 184: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" 184: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap 184: Test timeout computed to be: 1500 150: --------------------------------- 150: test O3A multithreading bug 150: 150: --------------------------------- 150: testCrippenO3A multithreading 150: 150: generating reference data 182: [15:23:56] ------------------------------------- 182: [15:23:56] testing PatternHolder 182: [15:23:56] ------------------------------------- 182: [15:23:56] testing TautomerPatternHolder 182: [15:23:56] ------------------------------------- 182: [15:23:56] testSegFaultInHolder 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] [15:23:56] SMILES Parse Error: check for mistakes around position 1:SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: syntax error while parsing: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] [15:23:56] SMILES Parse Error: check for mistakes around position SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf 182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: 182: [15:23:56] dsafsdf 182: [15:23:56] ^ 182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 182: [15:23:56] ------------------------------------- 182: [15:23:56] Results do not depend on numThreads 150: processing 150: launch :0 150: launch :1 150: launch :2 150: launch :3 163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: TOTAL Time elapsed 32.64 seconds 173/235 Test #163: testFMCS ............................... Passed 32.83 sec test 185 Start 185: testRGroupDecomp 185: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp 185: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 185: Test timeout computed to be: 1500 173: Query 0 185: [15:23:58] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters 185: [15:23:58] WARNING: not removing hydrogen atom with dummy atom neighbors 148: .........[15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: .[15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: .[15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() 185: iterative 185: bulk 185: bulk, no symmetry 182: [15:24:05] ------------------------------------- 182: [15:24:05] Results do not depend on numThreads (all same) 182: [15:24:06] ------------------------------------- 182: [15:24:06] testTautomerQueries 182: [15:24:06] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... 182: [15:24:06] ------------------------------------- 182: [15:24:06] github3881 recursive smarts with rings 174/235 Test #182: substructLibraryTest ................... Passed 19.80 sec test 186 Start 186: testRGroupDecompInternals 186: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals 186: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 186: Test timeout computed to be: 1500 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors 175/235 Test #186: testRGroupDecompInternals .............. Passed 0.22 sec test 187 Start 187: rgroupCatchTests 187: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests 187: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 187: Test timeout computed to be: 1500 185: [15:24:07] Relabelling existing label 187: Randomness seeded to: 1985732401 187: =============================================================================== 187: All tests passed (1475 assertions in 14 test cases) 187: 176/235 Test #187: rgroupCatchTests ....................... Passed 1.34 sec test 188 Start 188: pyRGroupDecomposition 188: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" 188: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap 188: Test timeout computed to be: 1500 185: Best mapping 173: Query 1 177/235 Test #185: testRGroupDecomp ....................... Passed 10.58 sec test 189 Start 189: molInterchangeTest1 189: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 189: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 189: Test timeout computed to be: 1500 189: [15:24:08] test1: basics 189: [15:24:08] done 189: [15:24:08] test2: basic writing 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"mol1 name","atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[0,0]}]}]} 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"z":9},{"stereo":"cw"},{"z":17},{"z":8,"impHs":1},{"impHs":3}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[1,4]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1}],"bonds":[{"bo":2,"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"bo":2,"atoms":[4,5]},{"atoms":[5,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","aromaticAtoms":[0,1,2,3,4,5],"aromaticBonds":[0,1,2,3,4,5],"cipRanks":[0,0,0,0,0,0],"atomRings":[[0,5,4,3,2,1]]}]}]} 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":3},{"impHs":2},{},{},{"z":7,"impHs":2},{"impHs":1},{},{"impHs":3},{"z":7},{"impHs":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[3,5]},{"bo":2,"atoms":[5,6]},{"atoms":[6,7]},{"atoms":[6,8]},{"bo":2,"atoms":[8,9]},{"atoms":[9,2]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","aromaticAtoms":[2,3,5,6,8,9],"aromaticBonds":[2,4,5,7,8,9],"cipRanks":[0,2,4,5,8,3,7,1,9,6],"atomRings":[[2,9,8,6,5,3]]}]}]} 189: [15:24:08] done 189: [15:24:08] test3: writing conformers 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"example 2","atoms":[{"z":8},{"stereo":"cw"},{"z":17,"isotope":35},{"z":9},{"z":1},{"z":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[0,4]},{"atoms":[1,5]}],"conformers":[{"dim":2,"coords":[[-1.1988,-0.0452],[-0.3332,0.4556],[0.166,1.322],[0.5332,-0.0438],[-2.0652,0.4542],[-0.834,1.3212]]},{"dim":3,"coords":[[0.9554,-0.3743,-0.4679],[-0.3616,-0.1311,-0.0795],[-0.5097,1.6256,0.1706],[-0.5779,-0.792,1.1042],[1.5277,0.1064,0.1628],[-1.0339,-0.4346,-0.8902]]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2024.09.6","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} 189: [15:24:08] done 189: [15:24:08] test4: writing properties 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"properties":{"foo_string":"bar","foo_int":1,"foo_double":1.2},"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[0,0]}]}]} 189: [15:24:08] done 189: [15:24:08] test5: writing partial charges 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"z":8,"impHs":1}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2024.09.6","values":[0.5,-0.5]}]}]} 189: [15:24:08] testing parse options 189: [15:24:08] done 189: [15:24:08] testing github #2046: CIPRank values from JSONDataToMols are not unsigned 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":2},{"impHs":2},{"impHs":2},{"z":8},{"impHs":1,"stereo":"cw"},{"z":9}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[4,5]},{"atoms":[4,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} 189: [15:24:08] done 189: [15:24:08] testing 'either' stereochemistry 189: [15:24:08] done 178/235 Test #189: molInterchangeTest1 .................... Passed 0.14 sec test 190 Start 190: molInterchangeCatchTest 190: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest 190: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 190: Test timeout computed to be: 1500 190: Randomness seeded to: 3774299301 190: [15:24:08] unrecognized bond type 12 set to zero while writing 190: [15:24:08] unrecognized bond type 0 set to zero while writing 190: =============================================================================== 190: All tests passed (125 assertions in 7 test cases) 190: 179/235 Test #190: molInterchangeCatchTest ................ Passed 0.06 sec test 191 Start 191: pyMolInterchange 191: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" 191: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap 191: Test timeout computed to be: 1500 191: .. 191: ---------------------------------------------------------------------- 191: Ran 2 tests in 0.019s 191: 191: OK 180/235 Test #191: pyMolInterchange ....................... Passed 0.65 sec test 192 Start 192: testSLNParse 192: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/testSLNParse 192: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse 192: Test timeout computed to be: 1500 192: Atoms: 192: 0 6 C chg: 1 deg: 5 exp: N/A imp: 0 hyb: 192: 1 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: 192: 2 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: 192: 3 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: 192: 4 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: 192: 5 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: 192: Bonds: 192: 0 0->1 order: 1 192: 1 0->2 order: 1 192: 2 0->3 order: 1 192: 3 0->4 order: 1 192: 4 0->5 order: 1 192: [15:24:09] SLN Parse Error: syntax error while parsing: CH4[I=13] 192: [15:24:09] Failed parsing SLN 'CH4[I=13]' 192: [15:24:09] SLN Parser error: Atom ID 1 appears *after* its ring closure. 192: [15:24:09] SLN Parser error: Ring closure 1 does not have a corresponding opener. 192: [15:24:09] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) 192: [15:24:09] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' 192: [15:24:09] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) 192: [15:24:09] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' 192: [15:24:09] SLN Parse Error: syntax error while parsing: CH4 fff 192: [15:24:09] Failed parsing SLN 'CH4 fff' 192: [15:24:09] SLN Parse Error: syntax error while parsing: C[charge=+1] foo 192: [15:24:09] Failed parsing SLN 'C[charge=+1] foo' 192: [15:24:09] Query property 'is' ignored on non-query atom 192: [15:24:09] Query property 'is' ignored on non-query atom 181/235 Test #192: testSLNParse ........................... Passed 0.25 sec test 193 Start 193: pySLNParse 193: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/Wrap/testSLN.py" 193: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap 193: Test timeout computed to be: 1500 148: ... 148: ---------------------------------------------------------------------- 148: Ran 22 tests in 48.637s 148: 148: OK 188: .................... 188: ---------------------------------------------------------------------- 188: Ran 20 tests in 1.307s 188: 188: OK 182/235 Test #188: pyRGroupDecomposition .................. Passed 2.29 sec test 194 Start 194: pyGraphMolWrap 194: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/rough_test.py" 194: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 194: Test timeout computed to be: 1500 193: .. 193: ---------------------------------------------------------------------- 193: Ran 2 tests in 0.018s 193: 193: OK 183/235 Test #148: pyDistGeomHelpers ...................... Passed 49.82 sec test 195 Start 195: pyTestConformerWrap 195: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testConformer.py" 195: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 195: Test timeout computed to be: 1500 184/235 Test #193: pySLNParse ............................. Passed 0.89 sec test 196 Start 196: pyTestTrajectory 196: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testTrajectory.py" 196: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 196: Test timeout computed to be: 1500 195: ...... 195: ---------------------------------------------------------------------- 195: Ran 6 tests in 0.057s 195: 195: OK 194: ..............[15:24:11] SMARTS Parse Error: syntax error while parsing: fiib 194: [15:24:11] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' 194: ....[15:24:11] ERROR: Problems encountered parsing data fields 194: [15:24:11] ERROR: moving to the beginning of the next molecule 194: [15:24:11] ERROR: Problems encountered parsing data fields 194: [15:24:11] ERROR: moving to the beginning of the next molecule 194: [15:24:11] Spurious data before the first property will be ignored 194: [15:24:11] Property will be truncated after the first blank line 194: [15:24:11] Property will be truncated after the first blank line 194: [15:24:11] Property will be truncated after the first blank line 194: [15:24:11] ERROR: Problems encountered parsing data fields 194: [15:24:11] ERROR: moving to the beginning of the next molecule 194: [15:24:11] ERROR: Problems encountered parsing data fields 194: [15:24:11] ERROR: moving to the beginning of the next molecule 194: [15:24:11] Spurious data before the first property will be ignored 194: [15:24:11] Property will be truncated after the first blank line 194: [15:24:11] Property will be truncated after the first blank line 194: [15:24:11] Property will be truncated after the first blank line 194: [15:24:11] ERROR: Problems encountered parsing data fields 194: [15:24:11] ERROR: moving to the beginning of the next molecule 194: [15:24:11] Property will be truncated after the first blank line 194: [15:24:11] ERROR: Problems encountered parsing data fields 194: [15:24:11] ERROR: moving to the beginning of the next molecule 194: [15:24:11] Property will be truncated after the first blank line 194: .[15:24:11] SMILES Parse Error: syntax error while parsing: fail 194: [15:24:11] SMILES Parse Error: check for mistakes around position 1: 194: [15:24:11] fail 194: [15:24:11] ^ 194: [15:24:11] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' 194: [15:24:11] ERROR: Smiles parse error on line 2 194: [15:24:11] ERROR: Cannot create molecule from : 'fail' 194: >>> This may result in an infinite loop. It should finish almost instantly 194: <<< OK, it finished. 196: [15:24:11] 196: 196: **** 196: Pre-condition Violation 196: from must be < size() 196: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 196: Failed Expression: from < static_cast(size()) 196: ---------- 196: Stacktrace: 196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 5# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 11# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 12# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 13# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 14# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 15# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 21# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005335D0 in /usr/bin/python3 196: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 26# 0x00000000004AC3B4 in /usr/bin/python3 196: 27# 0x0000000000665934 in /usr/bin/python3 196: 28# _PyObject_MakeTpCall in /usr/bin/python3 196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 30# 0x00000000005335D0 in /usr/bin/python3 196: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 32# 0x00000000004AC3B4 in /usr/bin/python3 196: 33# 0x0000000000665934 in /usr/bin/python3 196: 34# _PyObject_MakeTpCall in /usr/bin/python3 196: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 36# 0x00000000005335D0 in /usr/bin/python3 196: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 38# 0x00000000004AC3B4 in /usr/bin/python3 196: 39# 0x0000000000665934 in /usr/bin/python3 196: 40# _PyObject_MakeTpCall in /usr/bin/python3 196: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 42# 0x0000000000505090 in /usr/bin/python3 196: 43# _PyObject_MakeTpCall in /usr/bin/python3 196: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 45# PyEval_EvalCode in /usr/bin/python3 196: 46# 0x00000000005FFD24 in /usr/bin/python3 196: 47# 0x00000000005F9904 in /usr/bin/python3 196: 48# 0x0000000000627ED4 in /usr/bin/python3 196: 49# 0x0000000000627274 in /usr/bin/python3 196: 50# 0x0000000000627010 in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 196: 53# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: 196: .[15:24:11] 196: 196: **** 196: Pre-condition Violation 196: from must be < size() 196: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 196: Failed Expression: from < static_cast(size()) 196: ---------- 196: Stacktrace: 196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 5# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 11# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 12# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 13# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 14# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 15# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 21# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005335D0 in /usr/bin/python3 196: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 26# 0x00000000004AC3B4 in /usr/bin/python3 196: 27# 0x0000000000665934 in /usr/bin/python3 196: 28# _PyObject_MakeTpCall in /usr/bin/python3 196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 30# 0x00000000005335D0 in /usr/bin/python3 196: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 32# 0x00000000004AC3B4 in /usr/bin/python3 196: 33# 0x0000000000665934 in /usr/bin/python3 196: 34# _PyObject_MakeTpCall in /usr/bin/python3 196: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 36# 0x00000000005335D0 in /usr/bin/python3 196: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 38# 0x00000000004AC3B4 in /usr/bin/python3 196: 39# 0x0000000000665934 in /usr/bin/python3 196: 40# _PyObject_MakeTpCall in /usr/bin/python3 196: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 42# 0x0000000000505090 in /usr/bin/python3 196: 43# _PyObject_MakeTpCall in /usr/bin/python3 196: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 45# PyEval_EvalCode in /usr/bin/python3 196: 46# 0x00000000005FFD24 in /usr/bin/python3 196: 47# 0x00000000005F9904 in /usr/bin/python3 196: 48# 0x0000000000627ED4 in /usr/bin/python3 196: 49# 0x0000000000627274 in /usr/bin/python3 196: 50# 0x0000000000627010 in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 196: 53# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: 194: ............[15:24:11] Explicit valence for atom # 1 C, 5, is greater than permitted 185/235 Test #195: pyTestConformerWrap .................... Passed 1.02 sec test 197 Start 197: pyTestSGroups 197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testSGroups.py" 197: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 197: Test timeout computed to be: 1500 194: ......[15:24:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 194: [15:24:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 194: [15:24:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 194: [15:24:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 194: .inWedges: [H]C12C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H] |(-0.612,-0.6446,0.635;0.0021,-0.0041,0.002;-0.0187,1.5258,0.0104;-0.6498,2.1424,0.6504;1.5111,1.5466,-0.0041;2.1372,2.1804,0.624;1.5319,0.0168,-0.0125;2.175,-0.6067,0.6086;1.5173,0.025,-1.5424;2.1484,-0.5936,-2.1805;-0.0125,0.0041,-1.5279;-0.6405,-0.6297,-2.154;-0.0333,1.534,-1.5195;-0.6783,2.1574,-2.1387;1.4965,1.5548,-1.534;2.1106,2.1972,-2.1651)| 194: ........[15:24:11] non-ring atom 0 marked aromatic 194: [15:24:11] non-ring atom 0 marked aromatic 194: [15:24:11] 194: 194: **** 194: Range Error 194: idx 194: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp 194: Failed Expression: 12 < 6 194: ---------- 194: Stacktrace: 194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 194: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 194: 4# 0x0000FFFFB73A6C70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 6# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 194: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 17# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 18# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 19# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 20# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 27# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 28# _PyObject_MakeTpCall in /usr/bin/python3 194: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 30# 0x00000000005335D0 in /usr/bin/python3 194: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 32# 0x00000000004AC3B4 in /usr/bin/python3 194: 33# 0x0000000000665934 in /usr/bin/python3 194: 34# _PyObject_MakeTpCall in /usr/bin/python3 194: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 36# 0x00000000005335D0 in /usr/bin/python3 194: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 38# 0x00000000004AC3B4 in /usr/bin/python3 194: 39# 0x0000000000665934 in /usr/bin/python3 194: 40# _PyObject_MakeTpCall in /usr/bin/python3 194: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 42# 0x00000000005335D0 in /usr/bin/python3 194: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 44# 0x00000000004AC3B4 in /usr/bin/python3 194: 45# 0x0000000000665934 in /usr/bin/python3 194: 46# _PyObject_MakeTpCall in /usr/bin/python3 194: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 48# 0x0000000000505090 in /usr/bin/python3 194: 49# _PyObject_MakeTpCall in /usr/bin/python3 194: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 51# PyEval_EvalCode in /usr/bin/python3 194: 52# 0x00000000005FFD24 in /usr/bin/python3 194: 53# 0x00000000005F9904 in /usr/bin/python3 194: 54# 0x0000000000627ED4 in /usr/bin/python3 194: 55# 0x0000000000627274 in /usr/bin/python3 194: 56# 0x0000000000627010 in /usr/bin/python3 194: 57# Py_RunMain in /usr/bin/python3 194: 58# Py_BytesMain in /usr/bin/python3 194: 59# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 61# _start in /usr/bin/python3 194: ---------- 194: **** 194: 194: [15:24:11] non-ring atom 0 marked aromatic 194: [15:24:11] non-ring atom 0 marked aromatic 194: [15:24:11] 194: 194: **** 194: Range Error 194: idx 194: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp 194: Failed Expression: 12 < 6 194: ---------- 194: Stacktrace: 194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 194: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 194: 4# 0x0000FFFFB73A6C70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 6# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 194: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 17# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 18# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 19# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 20# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 27# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 28# _PyObject_MakeTpCall in /usr/bin/python3 194: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 30# 0x00000000005335D0 in /usr/bin/python3 194: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 32# 0x00000000004AC3B4 in /usr/bin/python3 194: 33# 0x0000000000665934 in /usr/bin/python3 194: 34# _PyObject_MakeTpCall in /usr/bin/python3 194: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 36# 0x00000000005335D0 in /usr/bin/python3 194: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 38# 0x00000000004AC3B4 in /usr/bin/python3 194: 39# 0x0000000000665934 in /usr/bin/python3 194: 40# _PyObject_MakeTpCall in /usr/bin/python3 194: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 42# 0x00000000005335D0 in /usr/bin/python3 194: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 44# 0x00000000004AC3B4 in /usr/bin/python3 194: 45# 0x0000000000665934 in /usr/bin/python3 194: 46# _PyObject_MakeTpCall in /usr/bin/python3 194: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 48# 0x0000000000505090 in /usr/bin/python3 194: 49# _PyObject_MakeTpCall in /usr/bin/python3 194: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 51# PyEval_EvalCode in /usr/bin/python3 194: 52# 0x00000000005FFD24 in /usr/bin/python3 194: 53# 0x00000000005F9904 in /usr/bin/python3 194: 54# 0x0000000000627ED4 in /usr/bin/python3 194: 55# 0x0000000000627274 in /usr/bin/python3 194: 56# 0x0000000000627010 in /usr/bin/python3 194: 57# Py_RunMain in /usr/bin/python3 194: 58# Py_BytesMain in /usr/bin/python3 194: 59# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 61# _start in /usr/bin/python3 194: ---------- 194: **** 194: 194: ...............[15:24:11] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. 194: [15:24:11] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. 196: .[15:24:11] 196: 196: **** 196: Range Error 196: snapshotNum 196: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 196: Failed Expression: 0 < 0 196: ---------- 196: Stacktrace: 196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 2# RDKit::Trajectory::getSnapshot(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 12# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 13# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 14# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 15# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 23# _PyObject_MakeTpCall in /usr/bin/python3 196: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 25# 0x00000000005335D0 in /usr/bin/python3 196: 26# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 27# 0x00000000004AC3B4 in /usr/bin/python3 196: 28# 0x0000000000665934 in /usr/bin/python3 196: 29# _PyObject_MakeTpCall in /usr/bin/python3 196: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 31# 0x00000000005335D0 in /usr/bin/python3 196: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 33# 0x00000000004AC3B4 in /usr/bin/python3 196: 34# 0x0000000000665934 in /usr/bin/python3 196: 35# _PyObject_MakeTpCall in /usr/bin/python3 196: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 37# 0x00000000005335D0 in /usr/bin/python3 196: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 39# 0x00000000004AC3B4 in /usr/bin/python3 196: 40# 0x0000000000665934 in /usr/bin/python3 196: 41# _PyObject_MakeTpCall in /usr/bin/python3 196: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 43# 0x0000000000505090 in /usr/bin/python3 196: 44# _PyObject_MakeTpCall in /usr/bin/python3 196: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 46# PyEval_EvalCode in /usr/bin/python3 196: 47# 0x00000000005FFD24 in /usr/bin/python3 196: 48# 0x00000000005F9904 in /usr/bin/python3 196: 49# 0x0000000000627ED4 in /usr/bin/python3 196: 50# 0x0000000000627274 in /usr/bin/python3 196: 51# 0x0000000000627010 in /usr/bin/python3 196: 52# Py_RunMain in /usr/bin/python3 196: 53# Py_BytesMain in /usr/bin/python3 196: 54# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 56# _start in /usr/bin/python3 196: ---------- 196: **** 196: 196: .[15:24:11] 196: 196: **** 196: Pre-condition Violation 196: The trajectory must have dimension == 3 196: Violation occurred on line 113 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 196: Failed Expression: traj.dimension() == 3 196: ---------- 196: Stacktrace: 196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 2# RDKit::readAmberTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 5# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 11# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 12# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 13# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 14# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 15# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 21# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005335D0 in /usr/bin/python3 196: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 26# 0x00000000004AC3B4 in /usr/bin/python3 196: 27# 0x0000000000665934 in /usr/bin/python3 196: 28# _PyObject_MakeTpCall in /usr/bin/python3 196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 30# 0x00000000005335D0 in /usr/bin/python3 196: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 32# 0x00000000004AC3B4 in /usr/bin/python3 196: 33# 0x0000000000665934 in /usr/bin/python3 196: 34# _PyObject_MakeTpCall in /usr/bin/python3 196: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 36# 0x00000000005335D0 in /usr/bin/python3 196: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 38# 0x00000000004AC3B4 in /usr/bin/python3 196: 39# 0x0000000000665934 in /usr/bin/python3 196: 40# _PyObject_MakeTpCall in /usr/bin/python3 196: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 42# 0x0000000000505090 in /usr/bin/python3 196: 43# _PyObject_MakeTpCall in /usr/bin/python3 196: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 45# PyEval_EvalCode in /usr/bin/python3 196: 46# 0x00000000005FFD24 in /usr/bin/python3 196: 47# 0x00000000005F9904 in /usr/bin/python3 196: 48# 0x0000000000627ED4 in /usr/bin/python3 196: 49# 0x0000000000627274 in /usr/bin/python3 196: 50# 0x0000000000627010 in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 196: 53# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: 196: ..[15:24:11] 196: 196: **** 196: Pre-condition Violation 196: The trajectory must have dimension == 3 196: Violation occurred on line 154 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 196: Failed Expression: traj.dimension() == 3 196: ---------- 196: Stacktrace: 196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 2# RDKit::readGromosTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 5# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 11# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 12# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 13# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 14# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 15# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 21# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005335D0 in /usr/bin/python3 196: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 26# 0x00000000004AC3B4 in /usr/bin/python3 196: 27# 0x0000000000665934 in /usr/bin/python3 196: 28# _PyObject_MakeTpCall in /usr/bin/python3 196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 30# 0x00000000005335D0 in /usr/bin/python3 196: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 32# 0x00000000004AC3B4 in /usr/bin/python3 196: 33# 0x0000000000665934 in /usr/bin/python3 196: 34# _PyObject_MakeTpCall in /usr/bin/python3 196: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 36# 0x00000000005335D0 in /usr/bin/python3 196: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 38# 0x00000000004AC3B4 in /usr/bin/python3 196: 39# 0x0000000000665934 in /usr/bin/python3 196: 40# _PyObject_MakeTpCall in /usr/bin/python3 196: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 42# 0x0000000000505090 in /usr/bin/python3 196: 43# _PyObject_MakeTpCall in /usr/bin/python3 196: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 45# PyEval_EvalCode in /usr/bin/python3 196: 46# 0x00000000005FFD24 in /usr/bin/python3 196: 47# 0x00000000005F9904 in /usr/bin/python3 196: 48# 0x0000000000627ED4 in /usr/bin/python3 196: 49# 0x0000000000627274 in /usr/bin/python3 196: 50# 0x0000000000627010 in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 196: 53# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: 196: .[15:24:11] 196: 196: **** 196: Pre-condition Violation 196: d_pos must not be NULL 196: Violation occurred on line 23 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 196: Failed Expression: d_pos 196: ---------- 196: Stacktrace: 196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 5# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 11# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 12# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 13# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 14# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 15# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 21# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005335D0 in /usr/bin/python3 196: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 26# 0x00000000004AC3B4 in /usr/bin/python3 196: 27# 0x0000000000665934 in /usr/bin/python3 196: 28# _PyObject_MakeTpCall in /usr/bin/python3 196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 30# 0x00000000005335D0 in /usr/bin/python3 196: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 32# 0x00000000004AC3B4 in /usr/bin/python3 196: 33# 0x0000000000665934 in /usr/bin/python3 196: 34# _PyObject_MakeTpCall in /usr/bin/python3 196: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 36# 0x00000000005335D0 in /usr/bin/python3 196: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 38# 0x00000000004AC3B4 in /usr/bin/python3 196: 39# 0x0000000000665934 in /usr/bin/python3 196: 40# _PyObject_MakeTpCall in /usr/bin/python3 196: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 42# 0x0000000000505090 in /usr/bin/python3 196: 43# _PyObject_MakeTpCall in /usr/bin/python3 196: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 45# PyEval_EvalCode in /usr/bin/python3 196: 46# 0x00000000005FFD24 in /usr/bin/python3 196: 47# 0x00000000005F9904 in /usr/bin/python3 196: 48# 0x0000000000627ED4 in /usr/bin/python3 196: 49# 0x0000000000627274 in /usr/bin/python3 196: 50# 0x0000000000627010 in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 196: 53# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: 196: [15:24:11] 196: 196: **** 196: Pre-condition Violation 196: d_trajectory must not be NULL 196: Violation occurred on line 24 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 196: Failed Expression: d_trajectory 196: ---------- 196: Stacktrace: 196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 5# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 11# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 12# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 13# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 14# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 15# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 21# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005335D0 in /usr/bin/python3 196: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 26# 0x00000000004AC3B4 in /usr/bin/python3 196: 27# 0x0000000000665934 in /usr/bin/python3 196: 28# _PyObject_MakeTpCall in /usr/bin/python3 196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 30# 0x00000000005335D0 in /usr/bin/python3 196: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 32# 0x00000000004AC3B4 in /usr/bin/python3 196: 33# 0x0000000000665934 in /usr/bin/python3 196: 34# _PyObject_MakeTpCall in /usr/bin/python3 196: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 36# 0x00000000005335D0 in /usr/bin/python3 196: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 38# 0x00000000004AC3B4 in /usr/bin/python3 196: 39# 0x0000000000665934 in /usr/bin/python3 196: 40# _PyObject_MakeTpCall in /usr/bin/python3 196: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 42# 0x0000000000505090 in /usr/bin/python3 196: 43# _PyObject_MakeTpCall in /usr/bin/python3 196: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 45# PyEval_EvalCode in /usr/bin/python3 196: 46# 0x00000000005FFD24 in /usr/bin/python3 196: 47# 0x00000000005F9904 in /usr/bin/python3 196: 48# 0x0000000000627ED4 in /usr/bin/python3 196: 49# 0x0000000000627274 in /usr/bin/python3 196: 50# 0x0000000000627010 in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 196: 53# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: 196: .[15:24:11] 196: 196: **** 196: Range Error 196: snapshotNum 196: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 196: Failed Expression: 5 < 5 196: ---------- 196: Stacktrace: 196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 2# RDKit::Trajectory::getSnapshot(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 12# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 13# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 14# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 15# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 23# _PyObject_MakeTpCall in /usr/bin/python3 196: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 25# 0x00000000005335D0 in /usr/bin/python3 196: 26# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 27# 0x00000000004AC3B4 in /usr/bin/python3 196: 28# 0x0000000000665934 in /usr/bin/python3 196: 29# _PyObject_MakeTpCall in /usr/bin/python3 196: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 31# 0x00000000005335D0 in /usr/bin/python3 196: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 33# 0x00000000004AC3B4 in /usr/bin/python3 196: 34# 0x0000000000665934 in /usr/bin/python3 196: 35# _PyObject_MakeTpCall in /usr/bin/python3 196: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 37# 0x00000000005335D0 in /usr/bin/python3 196: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 39# 0x00000000004AC3B4 in /usr/bin/python3 196: 40# 0x0000000000665934 in /usr/bin/python3 196: 41# _PyObject_MakeTpCall in /usr/bin/python3 196: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 43# 0x0000000000505090 in /usr/bin/python3 196: 44# _PyObject_MakeTpCall in /usr/bin/python3 196: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 46# PyEval_EvalCode in /usr/bin/python3 196: 47# 0x00000000005FFD24 in /usr/bin/python3 196: 48# 0x00000000005F9904 in /usr/bin/python3 196: 49# 0x0000000000627ED4 in /usr/bin/python3 196: 50# 0x0000000000627274 in /usr/bin/python3 196: 51# 0x0000000000627010 in /usr/bin/python3 196: 52# Py_RunMain in /usr/bin/python3 196: 53# Py_BytesMain in /usr/bin/python3 196: 54# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 56# _start in /usr/bin/python3 196: ---------- 196: **** 196: 196: [15:24:11] 196: 196: **** 196: Range Error 196: pointNum 196: Violation occurred on line 27 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 196: Failed Expression: 10 < 10 196: ---------- 196: Stacktrace: 196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 5# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 11# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 12# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 13# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 14# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 15# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 21# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005335D0 in /usr/bin/python3 196: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 26# 0x00000000004AC3B4 in /usr/bin/python3 196: 27# 0x0000000000665934 in /usr/bin/python3 196: 28# _PyObject_MakeTpCall in /usr/bin/python3 196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 30# 0x00000000005335D0 in /usr/bin/python3 196: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 32# 0x00000000004AC3B4 in /usr/bin/python3 196: 33# 0x0000000000665934 in /usr/bin/python3 196: 34# _PyObject_MakeTpCall in /usr/bin/python3 196: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 36# 0x00000000005335D0 in /usr/bin/python3 196: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 38# 0x00000000004AC3B4 in /usr/bin/python3 196: 39# 0x0000000000665934 in /usr/bin/python3 196: 40# _PyObject_MakeTpCall in /usr/bin/python3 196: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 42# 0x0000000000505090 in /usr/bin/python3 196: 43# _PyObject_MakeTpCall in /usr/bin/python3 196: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 45# PyEval_EvalCode in /usr/bin/python3 196: 46# 0x00000000005FFD24 in /usr/bin/python3 196: 47# 0x00000000005F9904 in /usr/bin/python3 196: 48# 0x0000000000627ED4 in /usr/bin/python3 196: 49# 0x0000000000627274 in /usr/bin/python3 196: 50# 0x0000000000627010 in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 196: 53# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: 196: .[15:24:11] 196: 196: **** 196: Range Error 196: snapshotNum 196: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 196: Failed Expression: 5 < 5 196: ---------- 196: Stacktrace: 196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 2# RDKit::Trajectory::getSnapshot(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 12# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 13# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 14# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 15# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 23# _PyObject_MakeTpCall in /usr/bin/python3 196: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 25# 0x00000000005335D0 in /usr/bin/python3 196: 26# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 27# 0x00000000004AC3B4 in /usr/bin/python3 196: 28# 0x0000000000665934 in /usr/bin/python3 196: 29# _PyObject_MakeTpCall in /usr/bin/python3 196: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 31# 0x00000000005335D0 in /usr/bin/python3 196: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 33# 0x00000000004AC3B4 in /usr/bin/python3 196: 34# 0x0000000000665934 in /usr/bin/python3 196: 35# _PyObject_MakeTpCall in /usr/bin/python3 196: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 37# 0x00000000005335D0 in /usr/bin/python3 196: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 39# 0x00000000004AC3B4 in /usr/bin/python3 196: 40# 0x0000000000665934 in /usr/bin/python3 196: 41# _PyObject_MakeTpCall in /usr/bin/python3 196: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 43# 0x0000000000505090 in /usr/bin/python3 196: 44# _PyObject_MakeTpCall in /usr/bin/python3 196: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 46# PyEval_EvalCode in /usr/bin/python3 196: 47# 0x00000000005FFD24 in /usr/bin/python3 196: 48# 0x00000000005F9904 in /usr/bin/python3 196: 49# 0x0000000000627ED4 in /usr/bin/python3 196: 50# 0x0000000000627274 in /usr/bin/python3 196: 51# 0x0000000000627010 in /usr/bin/python3 196: 52# Py_RunMain in /usr/bin/python3 196: 53# Py_BytesMain in /usr/bin/python3 196: 54# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 56# _start in /usr/bin/python3 196: ---------- 196: **** 196: 196: [15:24:11] 196: 196: **** 196: Pre-condition Violation 196: d_dimension must be == 2 196: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 196: Failed Expression: d_trajectory->dimension() == 2 196: ---------- 196: Stacktrace: 196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 5# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 11# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 12# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 13# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 14# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 15# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 21# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005335D0 in /usr/bin/python3 196: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 26# 0x00000000004AC3B4 in /usr/bin/python3 196: 27# 0x0000000000665934 in /usr/bin/python3 196: 28# _PyObject_MakeTpCall in /usr/bin/python3 196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 30# 0x00000000005335D0 in /usr/bin/python3 196: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 32# 0x00000000004AC3B4 in /usr/bin/python3 196: 33# 0x0000000000665934 in /usr/bin/python3 196: 34# _PyObject_MakeTpCall in /usr/bin/python3 196: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 36# 0x00000000005335D0 in /usr/bin/python3 196: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 38# 0x00000000004AC3B4 in /usr/bin/python3 196: 39# 0x0000000000665934 in /usr/bin/python3 196: 40# _PyObject_MakeTpCall in /usr/bin/python3 196: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 42# 0x0000000000505090 in /usr/bin/python3 196: 43# _PyObject_MakeTpCall in /usr/bin/python3 196: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 45# PyEval_EvalCode in /usr/bin/python3 196: 46# 0x00000000005FFD24 in /usr/bin/python3 196: 47# 0x00000000005F9904 in /usr/bin/python3 196: 48# 0x0000000000627ED4 in /usr/bin/python3 196: 49# 0x0000000000627274 in /usr/bin/python3 196: 50# 0x0000000000627010 in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 196: 53# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: 196: [15:24:11] 196: 196: **** 196: Pre-condition Violation 196: d_dimension must be == 2 196: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 196: Failed Expression: d_trajectory->dimension() == 2 196: ---------- 196: Stacktrace: 196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 5# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 11# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 12# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 13# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 14# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 15# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 21# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005335D0 in /usr/bin/python3 196: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 26# 0x00000000004AC3B4 in /usr/bin/python3 196: 27# 0x0000000000665934 in /usr/bin/python3 196: 28# _PyObject_MakeTpCall in /usr/bin/python3 196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 30# 0x00000000005335D0 in /usr/bin/python3 196: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 32# 0x00000000004AC3B4 in /usr/bin/python3 196: 33# 0x0000000000665934 in /usr/bin/python3 196: 34# _PyObject_MakeTpCall in /usr/bin/python3 196: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 36# 0x00000000005335D0 in /usr/bin/python3 196: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 38# 0x00000000004AC3B4 in /usr/bin/python3 196: 39# 0x0000000000665934 in /usr/bin/python3 196: 40# _PyObject_MakeTpCall in /usr/bin/python3 196: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 42# 0x0000000000505090 in /usr/bin/python3 196: 43# _PyObject_MakeTpCall in /usr/bin/python3 196: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 45# PyEval_EvalCode in /usr/bin/python3 196: 46# 0x00000000005FFD24 in /usr/bin/python3 196: 47# 0x00000000005F9904 in /usr/bin/python3 196: 48# 0x0000000000627ED4 in /usr/bin/python3 196: 49# 0x0000000000627274 in /usr/bin/python3 196: 50# 0x0000000000627010 in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 196: 53# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: 196: . 196: ---------------------------------------------------------------------- 196: Ran 9 tests in 0.426s 196: 196: OK 196: Testing Trajectory wrapper 194: ..............[15:24:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 194: [15:24:11] Explicit valence for atom # 1 C, 5, is greater than permitted 186/235 Test #196: pyTestTrajectory ....................... Passed 1.37 sec test 198 Start 198: pyTestThreads 198: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testThreads.py" 198: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 198: Test timeout computed to be: 1500 197: ............. 197: ---------------------------------------------------------------------- 197: Ran 13 tests in 0.078s 197: 197: OK 197: Testing SubstanceGroups wrapper 187/235 Test #197: pyTestSGroups .......................... Passed 1.18 sec test 199 Start 199: pyTestMultithreadedMolSupplier 199: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" 199: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 199: Test timeout computed to be: 1500 194: ............................[15:24:13] unable to set wavy bonds for double bonds: 3 194: .............[15:24:13] 194: 194: **** 194: Range Error 194: idx 194: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp 194: Failed Expression: 6 < 5 194: ---------- 194: Stacktrace: 194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 194: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 194: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 6# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 194: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 17# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 18# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 19# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 20# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 27# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 28# _PyObject_MakeTpCall in /usr/bin/python3 194: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 30# 0x00000000005335D0 in /usr/bin/python3 194: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 32# 0x00000000004AC3B4 in /usr/bin/python3 194: 33# 0x0000000000665934 in /usr/bin/python3 194: 34# _PyObject_MakeTpCall in /usr/bin/python3 194: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 36# 0x00000000005335D0 in /usr/bin/python3 194: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 38# 0x00000000004AC3B4 in /usr/bin/python3 194: 39# 0x0000000000665934 in /usr/bin/python3 194: 40# _PyObject_MakeTpCall in /usr/bin/python3 194: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 42# 0x00000000005335D0 in /usr/bin/python3 194: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 44# 0x00000000004AC3B4 in /usr/bin/python3 194: 45# 0x0000000000665934 in /usr/bin/python3 194: 46# _PyObject_MakeTpCall in /usr/bin/python3 194: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 48# 0x0000000000505090 in /usr/bin/python3 194: 49# _PyObject_MakeTpCall in /usr/bin/python3 194: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 51# PyEval_EvalCode in /usr/bin/python3 194: 52# 0x00000000005FFD24 in /usr/bin/python3 194: 53# 0x00000000005F9904 in /usr/bin/python3 194: 54# 0x0000000000627ED4 in /usr/bin/python3 194: 55# 0x0000000000627274 in /usr/bin/python3 194: 56# 0x0000000000627010 in /usr/bin/python3 194: 57# Py_RunMain in /usr/bin/python3 194: 58# Py_BytesMain in /usr/bin/python3 194: 59# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 61# _start in /usr/bin/python3 194: ---------- 194: **** 194: 199: .s. 199: ---------------------------------------------------------------------- 199: Ran 3 tests in 0.137s 199: 199: OK (skipped=1) 199: Testing Smiles and SD MultithreadedMolSupplier 188/235 Test #199: pyTestMultithreadedMolSupplier ......... Passed 1.12 sec test 200 Start 200: pyTestPropertyLists 200: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testPropertyLists.py" 200: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 200: Test timeout computed to be: 1500 173: Query 2 200: [15:24:14] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. 200: [15:24:14] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. 200: [15:24:14] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 200: .[15:24:14] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. 200: [15:24:14] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. 200: [15:24:14] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 200: ...[15:24:14] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. 200: [15:24:14] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. 200: [15:24:14] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 200: . 200: ---------------------------------------------------------------------- 200: Ran 5 tests in 0.037s 200: 200: OK 189/235 Test #200: pyTestPropertyLists .................... Passed 0.93 sec test 201 Start 201: pyCDXMLTest 201: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/test_cdxml.py" 201: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 201: Test timeout computed to be: 1500 201: . 201: ---------------------------------------------------------------------- 201: Ran 1 test in 0.023s 201: 201: OK 190/235 Test #201: pyCDXMLTest ............................ Passed 0.83 sec test 202 Start 202: molStandardizeTest 202: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest 202: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 202: Test timeout computed to be: 1500 194: ....................[15:24:16] Explicit valence for atom # 1 F, 2, is greater than permitted 194: [15:24:16] Explicit valence for atom # 6 F, 2, is greater than permitted 194: [15:24:16] Can't kekulize mol. Unkekulized atoms: 3 4 5 194: .................[15:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 184: ......[15:24:17] 184: 184: **** 184: Pre-condition Violation 184: RingInfo not initialized 184: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp 184: Failed Expression: df_init 184: ---------- 184: Stacktrace: 184: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 184: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 184: 2# RDKit::RingInfo::numAtomRings(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 184: 3# RDKit::AtomRingQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 184: 4# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 184: 5# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 184: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 184: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 184: 8# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 184: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 184: 10# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 184: 11# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 184: 12# 0x0000FFFF9118EB90 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 184: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 184: 14# 0x0000FFFF92BF2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 184: 15# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 184: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 184: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 184: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 184: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 184: 20# 0x0000FFFF910EB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 184: 21# 0x0000FFFF910EB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 184: 22# 0x0000FFFF910EB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 184: 23# 0x0000FFFF910EB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 184: 24# 0x0000FFFF910EB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 184: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 184: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 184: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 184: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 184: 29# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 184: 30# 0x0000FFFF92BEF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 184: 31# _PyObject_MakeTpCall in /usr/bin/python3 184: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 184: 33# 0x00000000005335D0 in /usr/bin/python3 184: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 184: 35# 0x00000000004AC3B4 in /usr/bin/python3 184: 36# 0x0000000000665934 in /usr/bin/python3 184: 37# _PyObject_MakeTpCall in /usr/bin/python3 184: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 184: 39# 0x00000000005335D0 in /usr/bin/python3 184: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 184: 41# 0x00000000004AC3B4 in /usr/bin/python3 184: 42# 0x0000000000665934 in /usr/bin/python3 184: 43# _PyObject_MakeTpCall in /usr/bin/python3 184: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 184: 45# 0x00000000005335D0 in /usr/bin/python3 184: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 184: 47# 0x00000000004AC3B4 in /usr/bin/python3 184: 48# 0x0000000000665934 in /usr/bin/python3 184: 49# _PyObject_MakeTpCall in /usr/bin/python3 184: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 184: 51# 0x0000000000505090 in /usr/bin/python3 184: 52# _PyObject_MakeTpCall in /usr/bin/python3 184: 53# _PyEval_EvalFrameDefault in /usr/bin/python3 184: 54# PyEval_EvalCode in /usr/bin/python3 184: 55# 0x00000000005FFD24 in /usr/bin/python3 184: 56# 0x00000000005F9904 in /usr/bin/python3 184: 57# 0x0000000000627ED4 in /usr/bin/python3 184: 58# 0x0000000000627274 in /usr/bin/python3 184: 59# 0x0000000000627010 in /usr/bin/python3 184: 60# Py_RunMain in /usr/bin/python3 184: 61# Py_BytesMain in /usr/bin/python3 184: 62# 0x0000FFFF935D229C in /lib/aarch64-linux-gnu/libc.so.6 184: 63# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 184: 64# _start in /usr/bin/python3 184: ---------- 184: **** 184: 184: [15:24:17] 184: 184: **** 184: Pre-condition Violation 184: RingInfo not initialized 184: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp 184: Failed Expression: df_init 184: ---------- 184: Stacktrace: 184: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 184: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 184: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 184: 3# 0x0000FFFF90C42FA8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 184: 4# Queries::EqualityQuery::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 184: 5# RDKit::bondCompat(RDKit::Bond const*, RDKit::Bond const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 184: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 184: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 184: 8# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 184: 9# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 184: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 184: 11# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 184: 12# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 184: 13# 0x0000FFFF9118EB90 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 184: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 184: 15# 0x0000FFFF92BF2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 184: 16# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 184: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 184: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 184: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 184: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 184: 21# 0x0000FFFF910EB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 184: 22# 0x0000FFFF910EB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 184: 23# 0x0000FFFF910EB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 184: 24# 0x0000FFFF910EB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 184: 25# 0x0000FFFF910EB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 184: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 184: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 184: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 184: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 184: 30# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 184: 31# 0x0000FFFF92BEF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 184: 32# _PyObject_MakeTpCall in /usr/bin/python3 184: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 184: 34# 0x00000000005335D0 in /usr/bin/python3 184: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 184: 36# 0x00000000004AC3B4 in /usr/bin/python3 184: 37# 0x0000000000665934 in /usr/bin/python3 184: 38# _PyObject_MakeTpCall in /usr/bin/python3 184: 39# _PyEval_EvalFrameDefault in /usr/bin/python3 184: 40# 0x00000000005335D0 in /usr/bin/python3 184: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 184: 42# 0x00000000004AC3B4 in /usr/bin/python3 184: 43# 0x0000000000665934 in /usr/bin/python3 184: 44# _PyObject_MakeTpCall in /usr/bin/python3 184: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 184: 46# 0x00000000005335D0 in /usr/bin/python3 184: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 184: 48# 0x00000000004AC3B4 in /usr/bin/python3 184: 49# 0x0000000000665934 in /usr/bin/python3 184: 50# _PyObject_MakeTpCall in /usr/bin/python3 184: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 184: 52# 0x0000000000505090 in /usr/bin/python3 184: 53# _PyObject_MakeTpCall in /usr/bin/python3 184: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 184: 55# PyEval_EvalCode in /usr/bin/python3 184: 56# 0x00000000005FFD24 in /usr/bin/python3 184: 57# 0x00000000005F9904 in /usr/bin/python3 184: 58# 0x0000000000627ED4 in /usr/bin/python3 184: 59# 0x0000000000627274 in /usr/bin/python3 184: 60# 0x0000000000627010 in /usr/bin/python3 184: 61# Py_RunMain in /usr/bin/python3 184: 62# Py_BytesMain in /usr/bin/python3 184: 63# 0x0000FFFF935D229C in /lib/aarch64-linux-gnu/libc.so.6 184: 64# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 184: 65# _start in /usr/bin/python3 184: ---------- 184: **** 184: 191/235 Test #202: molStandardizeTest ..................... Passed 4.11 sec test 203 Start 203: molNormalizeTest 203: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest 203: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 203: Test timeout computed to be: 1500 203: [15:24:19] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 203: [15:24:19] Initializing Normalizer 203: [15:24:19] Running Normalizer 203: [15:24:19] Rule applied: BrokenazidetoN=N+=N- 203: [15:24:19] Initializing Normalizer 203: [15:24:19] Running Normalizer 203: [15:24:19] Initializing Normalizer 203: [15:24:19] Running Normalizer 192/235 Test #203: molNormalizeTest ....................... Passed 0.10 sec test 204 Start 204: molValidateTest 204: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest 204: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 204: Test timeout computed to be: 1500 204: ERROR: [FeaturesValidation] Query atom 0 is not allowed 204: ERROR: [FeaturesValidation] Dummy atom 0 is not allowed 204: ERROR: [FeaturesValidation] Query bond 0 is not allowed 204: ERROR: [FeaturesValidation] Bond 0 of aromatic type is not allowed 204: ERROR: [FeaturesValidation] Bond 1 of aromatic type is not allowed 204: ERROR: [FeaturesValidation] Bond 2 of aromatic type is not allowed 204: ERROR: [FeaturesValidation] Bond 3 of aromatic type is not allowed 204: ERROR: [FeaturesValidation] Bond 5 of aromatic type is not allowed 204: ERROR: [FeaturesValidation] Bond 6 of aromatic type is not allowed 204: ERROR: [FeaturesValidation] Bond 2 of dative type is not allowed 204: ERROR: [FeaturesValidation] Bond 3 of dative type is not allowed 204: ERROR: [FeaturesValidation] Atom 2 with alias 'CF3' is not allowed 204: ERROR: [FeaturesValidation] Enhanced stereochemistry features are not allowed 204: ERROR: [StereoValidation] Atom 3 has both unknown and wedged/dashed stereo bonds. 204: here 204: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order. 204: there 204: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. 193/235 Test #204: molValidateTest ........................ Passed 0.04 sec test 205 Start 205: molChargeTest 205: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest 205: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 205: Test timeout computed to be: 1500 194/235 Test #205: molChargeTest .......................... Passed 0.06 sec test 206 Start 206: molTautomerTest 206: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest 206: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 206: Test timeout computed to be: 1500 206: [15:24:20] Tautomer enumeration stopped at 292 tautomers: max transforms reached 206: [15:24:20] Tautomer enumeration stopped at 292 tautomers: max transforms reached 206: [15:24:20] Tautomer enumeration stopped at 50 tautomers: max tautomers reached 206: [15:24:20] Tautomer enumeration stopped at 33 tautomers: canceled 206: Enumeration was canceled due to timeout (50 ms) 195/235 Test #198: pyTestThreads .......................... Passed 10.33 sec test 207 Start 207: molStandardizeSmallTest 207: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest 207: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 207: Test timeout computed to be: 1500 196/235 Test #207: molStandardizeSmallTest ................ Passed 0.12 sec test 208 Start 208: molFragmentTest 208: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest 208: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 208: Test timeout computed to be: 1500 208: [15:24:22] SMARTS Parse Error: syntax error while parsing: [Cl 208: [15:24:22] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' 197/235 Test #208: molFragmentTest ........................ Passed 0.09 sec test 209 Start 209: molStandardizeCatchTest 209: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest 209: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 209: Test timeout computed to be: 1500 209: Randomness seeded to: 2879556809 209: * - * - * - * m1 209: * - * - * - * m2 206: 375 206: Enumeration has completed 209: * - * - * - * m1 209: * - * - * - * m2 209: [15:24:23] Can't kekulize mol. Unkekulized atoms: 3 7 209: [15:24:23] Can't kekulize mol. Unkekulized atoms: 3 8 209: [15:24:23] Can't kekulize mol. Unkekulized atoms: 2 3 4 206: [15:24:23] Tautomer enumeration stopped at 63 tautomers: canceled 206: CN=c1cc[nH]cn1 206: CN=c1ccnc[nH]1 206: CNc1ccncn1 206: res: CNc1ccncn1 206: CN=c1cccc[nH]1 206: CNc1ccccn1 206: res: CNc1ccccn1 198/235 Test #206: molTautomerTest ........................ Passed 6.19 sec test 210 Start 210: molStandardizePipelineTest 210: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest 210: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 210: Test timeout computed to be: 1500 210: Randomness seeded to: 2563615675 210: 1 Counts line too short: '' on line4 210: 1 Could not instantiate a valid molecule from input 210: 8 Molecule has no atoms 210: [15:24:26] Explicit valence for atom # 1 N, 4, is greater than permitted 210: [15:24:26] Explicit valence for atom # 1 N, 4, is greater than permitted 210: 8 Explicit valence for atom # 1 N, 4, is greater than permitted 210: 128 An error occurred while preparing the molecule for standardization. 210: 8 The molecule contains an unknown isotope: 3C 210: 4 Query atom 0 is not allowed 210: 4 Bond 0 of aromatic type is not allowed 210: 4 Bond 1 of aromatic type is not allowed 210: 4 Bond 2 of aromatic type is not allowed 210: 4 Bond 3 of aromatic type is not allowed 210: 4 Bond 5 of aromatic type is not allowed 210: 4 Bond 6 of aromatic type is not allowed 210: 4 Bond 2 of dative type is not allowed 210: 4 Bond 3 of dative type is not allowed 210: 4 Enhanced stereochemistry features are not allowed 210: 8 The radical at atom 0 is not allowed 210: [15:24:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 210: 16 The molecule includes non-null Z coordinates 210: 32 Atom 0 too close to bond 2 210: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit 210: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds 210: 64 Atom 0 has adjacent stereo bonds with like orientation 210: [15:24:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 210: 16 The molecule includes non-null Z coordinates 210: 64 Atom 0 has adjacent stereo bonds with like orientation 210: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit 210: 8388608 One or more metal atoms were disconnected. 210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 210: 67108864 The protonation state was adjusted. 210: 16777216 The representation of some functional groups was adjusted. 210: 67108864 The protonation state was adjusted. 210: 16777216 The representation of some functional groups was adjusted. 210: 67108864 The protonation state was adjusted. 210: 16777216 The representation of some functional groups was adjusted. 210: 16777216 The representation of some functional groups was adjusted. 210: 67108864 The protonation state was adjusted. 210: 16777216 The representation of some functional groups was adjusted. 210: 67108864 The protonation state was adjusted. 210: 16777216 The representation of some functional groups was adjusted. 210: 67108864 The protonation state was adjusted. 210: 16777216 The representation of some functional groups was adjusted. 210: 67108864 The protonation state was adjusted. 210: 8388608 One or more metal atoms were disconnected. 210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 210: 67108864 The protonation state was adjusted. 210: 8388608 One or more metal atoms were disconnected. 210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 210: 67108864 The protonation state was adjusted. 210: 8388608 One or more metal atoms were disconnected. 210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 210: 67108864 The protonation state was adjusted. 210: 8388608 One or more metal atoms were disconnected. 210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 210: 67108864 The protonation state was adjusted. 210: 8388608 One or more metal atoms were disconnected. 210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 210: 67108864 The protonation state was adjusted. 210: 16777216 The "wavy" style of bond 4 was removed 210: 16777216 Double bond 1 was assigned an undefined/unknown stereochemical configuration 210: 16777216 The "wavy" style of bond 2 was removed 210: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 210: 16777216 The "wavy" style of bond 1 was removed 210: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 210: 16777216 The "wavy" style of bond 1 was removed 210: 16777216 The "wavy" style of bond 4 was removed 210: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 210: 16777216 The "wavy" style of bond 3 was removed 210: 16777216 The representation of some functional groups was adjusted. 210: [15:24:26] Can't kekulize mol. Unkekulized atoms: 2 3 5 210: =============================================================================== 210: All tests passed (268 assertions in 5 test cases) 210: 199/235 Test #210: molStandardizePipelineTest ............. Passed 0.72 sec test 211 Start 211: pyMolStandardize 211: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" 211: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap 211: Test timeout computed to be: 1500 194: ..[15:24:27] 194: 194: **** 194: Pre-condition Violation 194: no owner 194: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 194: Failed Expression: dp_mol 194: ---------- 194: Stacktrace: 194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector2 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 5# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 194: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so 194: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 16# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 17# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 18# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 19# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 20# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 26# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005335D0 in /usr/bin/python3 194: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 31# 0x00000000004AC3B4 in /usr/bin/python3 194: 32# 0x0000000000665934 in /usr/bin/python3 194: 33# _PyObject_MakeTpCall in /usr/bin/python3 194: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 35# 0x00000000005335D0 in /usr/bin/python3 194: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 37# 0x00000000004AC3B4 in /usr/bin/python3 194: 38# 0x0000000000665934 in /usr/bin/python3 194: 39# _PyObject_MakeTpCall in /usr/bin/python3 194: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 41# 0x00000000005335D0 in /usr/bin/python3 194: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 43# 0x00000000004AC3B4 in /usr/bin/python3 194: 44# 0x0000000000665934 in /usr/bin/python3 194: 45# _PyObject_MakeTpCall in /usr/bin/python3 194: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 47# 0x0000000000505090 in /usr/bin/python3 194: 48# _PyObject_MakeTpCall in /usr/bin/python3 194: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 50# PyEval_EvalCode in /usr/bin/python3 194: 51# 0x00000000005FFD24 in /usr/bin/python3 194: 52# 0x00000000005F9904 in /usr/bin/python3 194: 53# 0x0000000000627ED4 in /usr/bin/python3 194: 54# 0x0000000000627274 in /usr/bin/python3 194: 55# 0x0000000000627010 in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 194: 58# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: 194: [15:24:27] 194: 194: **** 194: Pre-condition Violation 194: no owner 194: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 194: Failed Expression: dp_mol 194: ---------- 194: Stacktrace: 194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 2# RDKit::AtomGetNeighbors(RDKit::Atom*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 5# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 194: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so 194: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 16# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 17# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 18# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 19# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 20# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 26# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005335D0 in /usr/bin/python3 194: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 31# 0x00000000004AC3B4 in /usr/bin/python3 194: 32# 0x0000000000665934 in /usr/bin/python3 194: 33# _PyObject_MakeTpCall in /usr/bin/python3 194: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 35# 0x00000000005335D0 in /usr/bin/python3 194: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 37# 0x00000000004AC3B4 in /usr/bin/python3 194: 38# 0x0000000000665934 in /usr/bin/python3 194: 39# _PyObject_MakeTpCall in /usr/bin/python3 194: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 41# 0x00000000005335D0 in /usr/bin/python3 194: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 43# 0x00000000004AC3B4 in /usr/bin/python3 194: 44# 0x0000000000665934 in /usr/bin/python3 194: 45# _PyObject_MakeTpCall in /usr/bin/python3 194: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 47# 0x0000000000505090 in /usr/bin/python3 194: 48# _PyObject_MakeTpCall in /usr/bin/python3 194: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 50# PyEval_EvalCode in /usr/bin/python3 194: 51# 0x00000000005FFD24 in /usr/bin/python3 194: 52# 0x00000000005F9904 in /usr/bin/python3 194: 53# 0x0000000000627ED4 in /usr/bin/python3 194: 54# 0x0000000000627274 in /usr/bin/python3 194: 55# 0x0000000000627010 in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 194: 58# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: 194: [15:24:27] 194: 194: **** 194: Pre-condition Violation 194: no owner 194: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 194: Failed Expression: dp_mol 194: ---------- 194: Stacktrace: 194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 2# RDKit::AtomGetBonds(RDKit::Atom*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 5# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 194: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so 194: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 16# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 17# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 18# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 19# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 20# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 26# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005335D0 in /usr/bin/python3 194: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 31# 0x00000000004AC3B4 in /usr/bin/python3 194: 32# 0x0000000000665934 in /usr/bin/python3 194: 33# _PyObject_MakeTpCall in /usr/bin/python3 194: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 35# 0x00000000005335D0 in /usr/bin/python3 194: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 37# 0x00000000004AC3B4 in /usr/bin/python3 194: 38# 0x0000000000665934 in /usr/bin/python3 194: 39# _PyObject_MakeTpCall in /usr/bin/python3 194: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 41# 0x00000000005335D0 in /usr/bin/python3 194: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 43# 0x00000000004AC3B4 in /usr/bin/python3 194: 44# 0x0000000000665934 in /usr/bin/python3 194: 45# _PyObject_MakeTpCall in /usr/bin/python3 194: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 47# 0x0000000000505090 in /usr/bin/python3 194: 48# _PyObject_MakeTpCall in /usr/bin/python3 194: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 50# PyEval_EvalCode in /usr/bin/python3 194: 51# 0x00000000005FFD24 in /usr/bin/python3 194: 52# 0x00000000005F9904 in /usr/bin/python3 194: 53# 0x0000000000627ED4 in /usr/bin/python3 194: 54# 0x0000000000627274 in /usr/bin/python3 194: 55# 0x0000000000627010 in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 194: 58# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: 194: [15:24:27] 194: 194: **** 194: Pre-condition Violation 194: no owner 194: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 194: Failed Expression: dp_mol 194: ---------- 194: Stacktrace: 194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 2# RDKit::AtomIsInRing(RDKit::Atom const*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 5# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 194: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so 194: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 16# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 17# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 18# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 19# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 20# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 26# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005335D0 in /usr/bin/python3 194: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 31# 0x00000000004AC3B4 in /usr/bin/python3 194: 32# 0x0000000000665934 in /usr/bin/python3 194: 33# _PyObject_MakeTpCall in /usr/bin/python3 194: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 35# 0x00000000005335D0 in /usr/bin/python3 194: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 37# 0x00000000004AC3B4 in /usr/bin/python3 194: 38# 0x0000000000665934 in /usr/bin/python3 194: 39# _PyObject_MakeTpCall in /usr/bin/python3 194: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 41# 0x00000000005335D0 in /usr/bin/python3 194: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 43# 0x00000000004AC3B4 in /usr/bin/python3 194: 44# 0x0000000000665934 in /usr/bin/python3 194: 45# _PyObject_MakeTpCall in /usr/bin/python3 194: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 47# 0x0000000000505090 in /usr/bin/python3 194: 48# _PyObject_MakeTpCall in /usr/bin/python3 194: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 50# PyEval_EvalCode in /usr/bin/python3 194: 51# 0x00000000005FFD24 in /usr/bin/python3 194: 52# 0x00000000005F9904 in /usr/bin/python3 194: 53# 0x0000000000627ED4 in /usr/bin/python3 194: 54# 0x0000000000627274 in /usr/bin/python3 194: 55# 0x0000000000627010 in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 194: 58# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: 194: [15:24:27] 194: 194: **** 194: Pre-condition Violation 194: no owner 194: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 194: Failed Expression: dp_mol 194: ---------- 194: Stacktrace: 194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 2# RDKit::AtomIsInRingSize(RDKit::Atom const*, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 5# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 194: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so 194: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 16# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 17# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 18# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 19# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 20# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 26# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005335D0 in /usr/bin/python3 194: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 31# 0x00000000004AC3B4 in /usr/bin/python3 194: 32# 0x0000000000665934 in /usr/bin/python3 194: 33# _PyObject_MakeTpCall in /usr/bin/python3 194: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 35# 0x00000000005335D0 in /usr/bin/python3 194: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 37# 0x00000000004AC3B4 in /usr/bin/python3 194: 38# 0x0000000000665934 in /usr/bin/python3 194: 39# _PyObject_MakeTpCall in /usr/bin/python3 194: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 41# 0x00000000005335D0 in /usr/bin/python3 194: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 43# 0x00000000004AC3B4 in /usr/bin/python3 194: 44# 0x0000000000665934 in /usr/bin/python3 194: 45# _PyObject_MakeTpCall in /usr/bin/python3 194: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 47# 0x0000000000505090 in /usr/bin/python3 194: 48# _PyObject_MakeTpCall in /usr/bin/python3 194: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 50# PyEval_EvalCode in /usr/bin/python3 194: 51# 0x00000000005FFD24 in /usr/bin/python3 194: 52# 0x00000000005F9904 in /usr/bin/python3 194: 53# 0x0000000000627ED4 in /usr/bin/python3 194: 54# 0x0000000000627274 in /usr/bin/python3 194: 55# 0x0000000000627010 in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 194: 58# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: 194: .....[15:24:27] 194: 194: **** 194: Range Error 194: atomIdx1 194: Violation occurred on line 496 in file ./Code/GraphMol/RWMol.cpp 194: Failed Expression: 0 < 0 194: ---------- 194: Stacktrace: 194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 194: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 5# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 194: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so 194: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 16# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 17# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 18# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 19# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 20# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 26# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005335D0 in /usr/bin/python3 194: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 31# 0x00000000004AC3B4 in /usr/bin/python3 194: 32# 0x0000000000665934 in /usr/bin/python3 194: 33# _PyObject_MakeTpCall in /usr/bin/python3 194: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 35# 0x00000000005335D0 in /usr/bin/python3 194: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 37# 0x00000000004AC3B4 in /usr/bin/python3 194: 38# 0x0000000000665934 in /usr/bin/python3 194: 39# _PyObject_MakeTpCall in /usr/bin/python3 194: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 41# 0x00000000005335D0 in /usr/bin/python3 194: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 43# 0x00000000004AC3B4 in /usr/bin/python3 194: 44# 0x0000000000665934 in /usr/bin/python3 194: 45# _PyObject_MakeTpCall in /usr/bin/python3 194: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 47# 0x0000000000505090 in /usr/bin/python3 194: 48# _PyObject_MakeTpCall in /usr/bin/python3 194: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 50# PyEval_EvalCode in /usr/bin/python3 194: 51# 0x00000000005FFD24 in /usr/bin/python3 194: 52# 0x00000000005F9904 in /usr/bin/python3 194: 53# 0x0000000000627ED4 in /usr/bin/python3 194: 54# 0x0000000000627274 in /usr/bin/python3 194: 55# 0x0000000000627010 in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 194: 58# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: 194: ......[15:24:27] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 194: [15:24:27] ERROR: Smiles parse error on line 0 194: [15:24:27] ERROR: Cannot create molecule from : 'c1ccccc' 194: [15:24:27] SMILES Parse Error: extra open parentheses while parsing: C(C 194: [15:24:27] SMILES Parse Error: check for mistakes around position 2: 194: [15:24:27] C(C 194: [15:24:27] ~^ 194: [15:24:27] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' 194: [15:24:27] ERROR: Smiles parse error on line 3 194: [15:24:27] ERROR: Cannot create molecule from : 'C(C' 194: [15:24:27] Explicit valence for atom # 1 C, 5, is greater than permitted 194: [15:24:27] ERROR: Could not sanitize molecule on line 6 194: [15:24:27] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted 194: [15:24:27] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 194: [15:24:27] ERROR: Smiles parse error on line 0 194: [15:24:27] ERROR: Cannot create molecule from : 'c1ccccc' 194: [15:24:27] SMILES Parse Error: extra open parentheses while parsing: C(C 194: [15:24:27] SMILES Parse Error: check for mistakes around position 2: 194: [15:24:27] C(C 194: [15:24:27] ~^ 194: [15:24:27] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' 194: [15:24:27] ERROR: Smiles parse error on line 3 194: [15:24:27] ERROR: Cannot create molecule from : 'C(C' 194: [15:24:27] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' 194: [15:24:27] ERROR: Smiles parse error on line 6 194: [15:24:27] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' 194: [15:24:27] Explicit valence for atom # 1 F, 2, is greater than permitted 194: [15:24:27] ERROR: Could not sanitize molecule ending on line 21 194: [15:24:27] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 194: [15:24:27] ERROR: EOF hit while reading atoms 194: [15:24:27] ERROR: moving to the beginning of the next molecule 194: [15:24:27] Explicit valence for atom # 1 F, 2, is greater than permitted 194: [15:24:27] ERROR: Could not sanitize molecule ending on line 21 194: [15:24:27] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 194: [15:24:27] ERROR: EOF hit while reading atoms 194: [15:24:27] ERROR: moving to the beginning of the next molecule 194: ....[15:24:27] 194: 194: **** 194: Pre-condition Violation 194: RingInfo not initialized 194: Violation occurred on line 170 in file ./Code/GraphMol/RingInfo.cpp 194: Failed Expression: df_init 194: ---------- 194: Stacktrace: 194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 2# RDKit::RingInfo::numRings() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 194: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 5# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 194: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so 194: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 16# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 17# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 18# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 19# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 20# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 26# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005335D0 in /usr/bin/python3 194: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 31# 0x00000000004AC3B4 in /usr/bin/python3 194: 32# 0x0000000000665934 in /usr/bin/python3 194: 33# _PyObject_MakeTpCall in /usr/bin/python3 194: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 35# 0x00000000005335D0 in /usr/bin/python3 194: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 37# 0x00000000004AC3B4 in /usr/bin/python3 194: 38# 0x0000000000665934 in /usr/bin/python3 194: 39# _PyObject_MakeTpCall in /usr/bin/python3 194: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 41# 0x00000000005335D0 in /usr/bin/python3 194: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 43# 0x00000000004AC3B4 in /usr/bin/python3 194: 44# 0x0000000000665934 in /usr/bin/python3 194: 45# _PyObject_MakeTpCall in /usr/bin/python3 194: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 47# 0x0000000000505090 in /usr/bin/python3 194: 48# _PyObject_MakeTpCall in /usr/bin/python3 194: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 50# PyEval_EvalCode in /usr/bin/python3 194: 51# 0x00000000005FFD24 in /usr/bin/python3 194: 52# 0x00000000005F9904 in /usr/bin/python3 194: 53# 0x0000000000627ED4 in /usr/bin/python3 194: 54# 0x0000000000627274 in /usr/bin/python3 194: 55# 0x0000000000627010 in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 194: 58# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: 194: .............[15:24:27] 194: 194: **** 194: Range Error 194: idx 194: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp 194: Failed Expression: 3 < 1 194: ---------- 194: Stacktrace: 194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 194: 3# boost::python::objects::caller_py_function_impl >, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 5# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 194: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 194: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so 194: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 16# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 17# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 18# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 19# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 20# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 26# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005335D0 in /usr/bin/python3 194: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 31# 0x00000000004AC3B4 in /usr/bin/python3 194: 32# 0x0000000000665934 in /usr/bin/python3 194: 33# _PyObject_MakeTpCall in /usr/bin/python3 194: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 35# 0x00000000005335D0 in /usr/bin/python3 194: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 37# 0x00000000004AC3B4 in /usr/bin/python3 194: 38# 0x0000000000665934 in /usr/bin/python3 194: 39# _PyObject_MakeTpCall in /usr/bin/python3 194: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 41# 0x00000000005335D0 in /usr/bin/python3 194: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 43# 0x00000000004AC3B4 in /usr/bin/python3 194: 44# 0x0000000000665934 in /usr/bin/python3 194: 45# _PyObject_MakeTpCall in /usr/bin/python3 194: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 47# 0x0000000000505090 in /usr/bin/python3 194: 48# _PyObject_MakeTpCall in /usr/bin/python3 194: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 50# PyEval_EvalCode in /usr/bin/python3 194: 51# 0x00000000005FFD24 in /usr/bin/python3 194: 52# 0x00000000005F9904 in /usr/bin/python3 194: 53# 0x0000000000627ED4 in /usr/bin/python3 194: 54# 0x0000000000627274 in /usr/bin/python3 194: 55# 0x0000000000627010 in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 194: 58# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: 194: ...[15:24:27] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 150: --------------------------------- 150: test getO3AForProbeConfs 150: 150: *********************************************************** 200/235 Test #150: testO3AAlign ........................... Passed 66.38 sec test 212 Start 212: testScaffoldNetwork 212: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork 212: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork 212: Test timeout computed to be: 1500 194: ............................[15:24:28] SMILES Parse Error: unclosed ring for input: 'C1CC' 194: ......smi: CC1=C(n2cccc2[C@H](C)Cl)C(C)CCC1 |(2.679,0.4142,;1.3509,1.181,;0.0229,0.4141,;0.0229,-1.1195,;1.2645,-2.0302,;0.7901,-3.4813,;-0.7446,-3.4813,;-1.219,-2.0302,;-2.679,-1.5609,;-3.0039,-0.0556,;-3.8202,-2.595,;-1.3054,1.1809,;-2.6335,0.4141,;-1.3054,2.7145,;0.0229,3.4813,;1.3509,2.7146,),wD:8.9,2.11,a:2,&1:8| 194: 561 194: ..[15:24:28] WARNING: not removing hydrogen atom without neighbors 194: [15:24:28] WARNING: not removing hydrogen atom with dummy atom neighbors 194: [15:24:28] WARNING: not removing hydrogen atom with wedged bond 194: [15:24:28] WARNING: not removing hydrogen atom without neighbors 194: [15:24:28] WARNING: not removing hydrogen atom with dummy atom neighbors 194: ......[15:24:28] Explicit valence for atom # 1 F, 2, is greater than permitted 194: [15:24:28] Can't kekulize mol. Unkekulized atoms: 0 1 2 194: .[15:24:28] Explicit valence for atom # 1 F, 2, is greater than permitted 194: [15:24:28] Explicit valence for atom # 1 F, 2, is greater than permitted 194: [15:24:28] Explicit valence for atom # 1 F, 2, is greater than permitted 194: [15:24:28] Explicit valence for atom # 1 F, 2, is greater than permitted 194: [15:24:28] Can't kekulize mol. Unkekulized atoms: 0 1 2 194: [15:24:28] Can't kekulize mol. Unkekulized atoms: 0 1 2 194: [15:24:28] Can't kekulize mol. Unkekulized atoms: 0 1 2 211: .....[15:24:28] Tautomer enumeration stopped at 292 tautomers: max transforms reached 194: ..........[15:24:29] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname 194: [15:24:29] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' 194: .[15:24:29] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname 194: [15:24:29] SMILES Parse Error: check for mistakes around position 4: 194: [15:24:29] CCC |$foo;;bar$| ourname 194: [15:24:29] ~~~^ 194: [15:24:29] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' 194: ..[15:24:29] SMILES Parse Error: syntax error while parsing: error 194: [15:24:29] SMILES Parse Error: check for mistakes around position 1: 194: [15:24:29] error 194: [15:24:29] ^ 194: [15:24:29] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' 194: [15:24:29] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' 194: [15:24:29] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' 194: [15:24:29] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' 211: [15:24:29] Tautomer enumeration stopped at 50 tautomers: max tautomers reached 194: .........................[15:24:29] SMILES Parse Error: syntax error while parsing: garbage_0 194: [15:24:29] SMILES Parse Error: check for mistakes around position 1: 194: [15:24:29] garbage_0 194: [15:24:29] ^ 194: [15:24:29] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' 194: [15:24:29] SMILES Parse Error: syntax error while parsing: garbage_2 194: [15:24:29] SMILES Parse Error: check for mistakes around position 1: 194: [15:24:29] garbage_2 194: [15:24:29] ^ 194: [15:24:29] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' 194: [15:24:29] SMILES Parse Error: syntax error while parsing: garbage_4 194: [15:24:29] SMILES Parse Error: check for mistakes around position 1: 194: [15:24:29] garbage_4 194: [15:24:29] ^ 194: [15:24:29] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' 194: ............ 194: ---------------------------------------------------------------------- 194: Ran 279 tests in 18.187s 194: 194: OK 194: supplier: 194: supplier: 194: supplier: 201/235 Test #194: pyGraphMolWrap ......................... Passed 19.40 sec test 213 Start 213: pyScaffoldNetwork 213: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" 213: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 213: Test timeout computed to be: 1500 211: .[15:24:30] Tautomer enumeration stopped at 21 tautomers: canceled 211: Enumeration was canceled due to timeout (50 ms) 213: ....... 213: ---------------------------------------------------------------------- 213: Ran 7 tests in 0.169s 213: 213: OK 202/235 Test #213: pyScaffoldNetwork ...................... Passed 1.48 sec test 214 Start 214: pyScaffoldNetworkPickling 214: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" 214: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 214: Test timeout computed to be: 1500 212: Randomness seeded to: 1858183942 212: =============================================================================== 212: All tests passed (273 assertions in 19 test cases) 212: 203/235 Test #212: testScaffoldNetwork .................... Passed 3.67 sec test 215 Start 215: testMolEnumerator 215: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator 215: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator 215: Test timeout computed to be: 1500 215: Randomness seeded to: 3481345342 215: [15:24:31] can only enumerate SRUs with CONNECT=HT or CONNECT=HH 211: Enumeration has completed 147: [15:24:31] UFFTYPER: Unrecognized atom type: S_6+6 (0) 147: [15:24:31] UFFTYPER: Warning: hybridization set to SP3 for atom 0 147: [15:24:31] UFFTYPER: Unrecognized charge state for atom: 0 211: [15:24:31] Tautomer enumeration stopped at 31 tautomers: canceled 215: =============================================================================== 215: All tests passed (321 assertions in 16 test cases) 215: 204/235 Test #215: testMolEnumerator ...................... Passed 0.36 sec test 216 Start 216: pyMolEnumerator 216: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" 216: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap 216: Test timeout computed to be: 1500 214: . 214: ---------------------------------------------------------------------- 214: Ran 1 test in 0.036s 214: 214: OK 205/235 Test #214: pyScaffoldNetworkPickling .............. Passed 1.19 sec test 217 Start 217: testAbbreviations 217: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations 217: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations 217: Test timeout computed to be: 1500 211: ..........[15:24:32] Explicit valence for atom # 1 N, 4, is greater than permitted 211: [15:24:32] Explicit valence for atom # 1 N, 4, is greater than permitted 211: [15:24:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: Randomness seeded to: 1593005015 217: [15:24:32] SMARTS Parse Error: syntax error while parsing: *fail 217: [15:24:32] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' 217: [15:24:32] no suitable SubstanceGroups found 217: =============================================================================== 217: All tests passed (195 assertions in 12 test cases) 217: 206/235 Test #217: testAbbreviations ...................... Passed 0.17 sec test 218 Start 218: pyAbbreviations 218: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" 218: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap 218: Test timeout computed to be: 1500 211: [15:24:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 216: ... 216: ---------------------------------------------------------------------- 216: Ran 3 tests in 0.056s 216: 216: OK 207/235 Test #216: pyMolEnumerator ........................ Passed 1.23 sec test 219 Start 219: generalizedSubstructCatch 219: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch 219: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct 219: Test timeout computed to be: 1500 218: ....... 218: ---------------------------------------------------------------------- 218: Ran 7 tests in 0.071s 218: 218: OK 208/235 Test #218: pyAbbreviations ........................ Passed 1.27 sec test 220 Start 220: pyGeneralizedSubstruct 220: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" 220: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap 220: Test timeout computed to be: 1500 219: Randomness seeded to: 2719601452 219: =============================================================================== 219: All tests passed (486 assertions in 10 test cases) 219: 209/235 Test #219: generalizedSubstructCatch .............. Passed 1.07 sec test 221 Start 221: testMolProcessing 221: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing 221: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing 221: Test timeout computed to be: 1500 220: ....... 220: ---------------------------------------------------------------------- 220: Ran 7 tests in 0.534s 220: 220: OK 210/235 Test #220: pyGeneralizedSubstruct ................. Passed 1.59 sec test 222 Start 222: pyMolProcessing 222: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py" 222: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap 222: Test timeout computed to be: 1500 211: ............[15:24:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 211: [15:24:35] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. 211: [15:24:35] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. 211: ........[15:24:36] Explicit valence for atom # 1 O, 3, is greater than permitted 211: .. 211: ---------------------------------------------------------------------- 211: Ran 38 tests in 9.125s 211: 211: OK 211: done 222: .. 222: ---------------------------------------------------------------------- 222: Ran 2 tests in 0.735s 222: 222: OK 211/235 Test #211: pyMolStandardize ....................... Passed 10.53 sec test 223 Start 223: testMIF 223: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/testMIF 223: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields 223: Test timeout computed to be: 1500 212/235 Test #222: pyMolProcessing ........................ Passed 1.97 sec test 224 Start 224: pyMIF 224: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/Wrap/testMIF.py" 224: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap 224: Test timeout computed to be: 1500 223: Randomness seeded to: 3058970526 223: =============================================================================== 223: All tests passed (27926 assertions in 8 test cases) 223: 213/235 Test #223: testMIF ................................ Passed 0.28 sec test 225 Start 225: testQuery 225: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Query/testQuery 225: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Query 225: Test timeout computed to be: 1500 225: Query 225: Query2 225: Equality 225: Greater 225: GreaterEqual 225: Less 225: LessEqual 225: Open Range 225: Closed Range 225: Float 225: With Tolerance 225: Set 225: And 225: Or 225: XOr 225: pointer and copy foo 225: Set2 214/235 Test #225: testQuery .............................. Passed 0.08 sec test 226 Start 226: testBaseFeatures 226: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Features/testBaseFeatures 226: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Features 226: Test timeout computed to be: 1500 226: ------------------------------------- 226: Basics for ExplicitFeatures. 226: done 226: ------------------------------------- 226: Basics for ImplicitFeatures. 226: done 226: ------------------------------------- 226: ExplicitFeatures 2D, string type. 226: done 215/235 Test #226: testBaseFeatures ....................... Passed 0.03 sec test 227 Start 227: testMatCalc 227: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc 227: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc 227: Test timeout computed to be: 1500 227: 1.68022e+08 227: 1.73149e+08 227: 1.05549e+08 227: 7.20603e+07 227: 1.41535e+08 227: 1.08592e+08 227: 1.11334e+08 227: 2.05553e+08 227: 1.54962e+08 227: 8.08231e+07 227: 5.61421e+07 227: 1.28874e+08 227: 1.59011e+08 227: 8.69902e+07 227: 1.31367e+08 227: 2.27389e+08 227: 1.60289e+08 227: 7.79813e+07 227: 1.61001e+08 227: 2.07599e+08 227: 2.24432e+08 227: 1.39725e+08 227: 2.42614e+08 227: 1.77578e+08 227: 1.05908e+08 227: 9.06742e+07 227: 1.8087e+08 227: 1.98182e+08 227: 2.03052e+08 227: 1.7673e+08 227: 9.32798e+07 227: 1.37969e+08 227: 1.83778e+08 227: 2.1228e+08 227: 5.06157e+07 227: 1.566e+08 227: 2.37142e+08 227: 1.49345e+08 227: 7.05819e+07 227: 1.71633e+08 227: 1.96817e+08 227: 2.18246e+08 227: 9.49496e+07 227: 2.25618e+08 227: 1.30219e+08 216/235 Test #227: testMatCalc ............................ Passed 0.03 sec test 228 Start 228: pyMatCalc 228: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" 228: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap 228: Test timeout computed to be: 1500 224: ....... 224: ---------------------------------------------------------------------- 224: Ran 7 tests in 0.194s 224: 224: OK 224: Testing MIF wrapper 217/235 Test #224: pyMIF .................................. Passed 1.36 sec test 229 Start 229: testSimDivPickers 229: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/testSimDivPickers 229: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers 229: Test timeout computed to be: 1500 229: [15:24:38] ------------------------------------- 229: [15:24:38] Testing github issue 1421: MaxMinPicker picking non-existent element. 229: [15:24:38] Done 229: [15:24:38] ------------------------------------- 229: [15:24:38] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. 229: [15:24:38] Done 218/235 Test #229: testSimDivPickers ...................... Passed 0.05 sec test 230 Start 230: pickersTestsCatch 230: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/pickersTestsCatch 230: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers 230: Test timeout computed to be: 1500 184: ............. 184: ---------------------------------------------------------------------- 184: Ran 19 tests in 44.490s 184: 184: OK 184: Testing atom rings 184: testing bond rings 184: searching atom rings 184: searching bond rings 184: done 219/235 Test #184: pySubstructLibrary ..................... Passed 45.92 sec test 231 Start 231: pySimDivPickers 231: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/Wrap/testPickers.py" 231: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap 231: Test timeout computed to be: 1500 230: Randomness seeded to: 187119721 230: =============================================================================== 230: All tests passed (21267 assertions in 1 test case) 230: 220/235 Test #230: pickersTestsCatch ...................... Passed 0.73 sec test 232 Start 232: pyRanker 232: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory/Wrap/testRanker.py" 232: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap 232: Test timeout computed to be: 1500 221: Randomness seeded to: 3426064245 221: =============================================================================== 221: All tests passed (203 assertions in 1 test case) 221: 221/235 Test #221: testMolProcessing ...................... Passed 5.40 sec test 233 Start 233: testChemicalFeatures 233: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures 233: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures 233: Test timeout computed to be: 1500 233: ----------------------------------------- 233: Test1 233: Done 222/235 Test #233: testChemicalFeatures ................... Passed 0.03 sec test 234 Start 234: pyFeatures 234: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/Wrap/testFeatures.py" 234: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap 234: Test timeout computed to be: 1500 231: [15:24:39] the useCache argument is deprecated and ignored 228: ..... 228: ---------------------------------------------------------------------- 228: Ran 5 tests in 1.754s 228: 228: OK 231: ...[15:24:40] the useCache argument is deprecated and ignored 231: [15:24:40] the useCache argument is deprecated and ignored 231: .[15:24:40] the useCache argument is deprecated and ignored 232: ..[15:24:40] 232: 232: **** 234: .. 234: ---------------------------------------------------------------------- 234: Ran 2 tests in 0.001s 234: 234: OK 234: Testing ChemicalFeatures Wrapper code: 232: Invariant Violation 232: Can't rank more bits than the ensemble size 232: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp 232: Failed Expression: num <= dp_maskBits->getNumOnBits() 232: ---------- 232: Stacktrace: 232: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 232: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 232: 2# RDInfoTheory::InfoBitRanker::getTopN(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitInfoTheory.so.1 232: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 232: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 232: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 232: 6# 0x0000FFFFAAE52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 232: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 232: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 232: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 232: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 232: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 232: 12# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 232: 13# 0x0000FFFFAAE4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 232: 14# _PyObject_MakeTpCall in /usr/bin/python3 232: 15# _PyEval_EvalFrameDefault in /usr/bin/python3 232: 16# 0x00000000005335D0 in /usr/bin/python3 232: 17# _PyEval_EvalFrameDefault in /usr/bin/python3 232: 18# 0x00000000004AC3B4 in /usr/bin/python3 232: 19# 0x0000000000665934 in /usr/bin/python3 232: 20# _PyObject_MakeTpCall in /usr/bin/python3 232: 21# _PyEval_EvalFrameDefault in /usr/bin/python3 232: 22# 0x00000000005335D0 in /usr/bin/python3 232: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 232: 24# 0x00000000004AC3B4 in /usr/bin/python3 232: 25# 0x0000000000665934 in /usr/bin/python3 232: 26# _PyObject_MakeTpCall in /usr/bin/python3 232: 27# _PyEval_EvalFrameDefault in /usr/bin/python3 232: 28# 0x00000000005335D0 in /usr/bin/python3 232: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 232: 30# 0x00000000004AC3B4 in /usr/bin/python3 232: 31# 0x0000000000665934 in /usr/bin/python3 232: 32# _PyObject_MakeTpCall in /usr/bin/python3 232: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 232: 34# 0x0000000000505090 in /usr/bin/python3 232: 35# _PyObject_MakeTpCall in /usr/bin/python3 232: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 232: 37# PyEval_EvalCode in /usr/bin/python3 232: 38# 0x00000000005FFD24 in /usr/bin/python3 232: 39# 0x00000000005F9904 in /usr/bin/python3 232: 40# 0x0000000000627ED4 in /usr/bin/python3 232: 41# 0x0000000000627274 in /usr/bin/python3 232: 42# 0x0000000000627010 in /usr/bin/python3 232: 43# Py_RunMain in /usr/bin/python3 232: 44# Py_BytesMain in /usr/bin/python3 232: 45# 0x0000FFFFAC77229C in /lib/aarch64-linux-gnu/libc.so.6 232: 46# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 232: 47# _start in /usr/bin/python3 232: ---------- 232: **** 232: 232: ... 232: ---------------------------------------------------------------------- 232: Ran 5 tests in 0.088s 232: 232: OK 223/235 Test #228: pyMatCalc .............................. Passed 2.64 sec test 235 Start 235: pythonProjectTests 235: Test command: /usr/bin/python3 "-m" "pytest" 235: Working Directory: /build/reproducible-path/rdkit-202409.6/Projects 235: Test timeout computed to be: 1500 224/235 Test #232: pyRanker ............................... Passed 1.03 sec 225/235 Test #234: pyFeatures ............................. Passed 0.76 sec 231: ....... 231: ---------------------------------------------------------------------- 231: Ran 11 tests in 3.026s 231: 231: OK 226/235 Test #231: pySimDivPickers ........................ Passed 3.89 sec 235: ============================= test session starts ============================== 235: platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 235: rootdir: /build/reproducible-path/rdkit-202409.6/Projects 235: configfile: pytest.ini 235: collected 12 items 235: 170: [15:24:50] Timed out after 71 seconds. 146: [15:25:04] done 146: [15:25:04] --------------------------------- 146: [15:25:04] test github issue 256: handling of zero-atom molecules 146: 146: [15:25:04] --------------------------------- 146: [15:25:04] test embedder callback function 146: [15:25:04] --------------------------------- 146: [15:25:04] test multi-threaded multi-conf embedding 146: 146: [15:25:11] --------------------------------- 146: [15:25:11] test github issue 563: Incorrect ring stereochemistry after embedding 146: 146: CNC[C@H]1CC[C@H](C[NH3+])CC1 209: [15:25:12] Explicit valence for atom # 0 Br, 1, is greater than permitted 209: =============================================================================== 209: All tests passed (38344 assertions in 51 test cases) 209: 227/235 Test #209: molStandardizeCatchTest ................ Passed 50.47 sec 146: [15:25:13] --------------------------------- 146: [15:25:13] test github issue 568: Incorrect stereochemistry after embedding 146: 146: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 146: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 146: O=C(CCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@H]1C(=O)OC(=O)[C@H]12 146: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 146: Nc1ncnc2c1ncn2[C@@H]1C=C(CO)[C@@H](O)[C@H]1O 33: [15:25:16] Finished 33: [15:25:16] ------------------------------------- 33: [15:25:16] Test github1843: RWMol.clear() should not destroy ring pointer. 33: [15:25:16] Finished 33: [15:25:16] ------------------------------------- 33: [15:25:16] Test Github 6370: non-physical radical counts being preserved 33: [15:25:16] Finished 228/235 Test #33: graphmolTest1 .......................... Passed 131.73 sec 146: CO[C@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 146: CO[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 146: CCS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 146: CCCCC[C@H](O)/C=C/[C@@]1(F)[C@H](O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)OC 146: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O 146: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 146: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 146: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 146: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 146: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 146: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O 146: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O 146: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O 146: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 147: [15:25:27] Interrupted, cancelling conformer generation 147: Atoms: 147: 0 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: SP3 chi: CCW nbrs:[9 3 1 6] 147: 1 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: SP3 chi: CCW nbrs:[0 13 6 7] 147: 2 7 N chg: 0 deg: 3 exp: 3 imp: 0 hyb: SP2 arom?: 1 147: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 147: 4 7 N chg: 0 deg: 1 exp: 1 imp: 2 hyb: SP3 147: 5 6 C chg: 0 deg: 3 exp: 3 imp: 1 hyb: SP3 chi: CW nbrs:[4 11 7] 147: 6 7 N chg: 0 deg: 2 exp: 2 imp: 0 hyb: SP3 rad: 1 147: 7 7 N chg: 0 deg: 2 exp: 2 imp: 1 hyb: SP3 147: 8 7 N chg: 0 deg: 3 exp: 3 imp: 0 hyb: SP2 arom?: 1 147: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP3 147: 10 8 O chg: 0 deg: 1 exp: 2 imp: 0 hyb: SP2 147: 11 7 N chg: 0 deg: 2 exp: 2 imp: 1 hyb: SP2 147: 12 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 147: 13 8 O chg: 0 deg: 1 exp: 1 imp: 0 hyb: SP3 rad: 1 147: Bonds: 147: 0 0->9 order: 1 147: 1 0->3 order: 1 147: 2 1->0 order: 1 147: 3 1->13 order: 1 147: 4 2->8 order: a conj?: 1 aromatic?: 1 147: 5 2->12 order: a conj?: 1 aromatic?: 1 147: 6 3->10 order: 2 conj?: 1 147: 7 3->8 order: 1 conj?: 1 147: 8 5->4 order: 1 147: 9 11->5 order: 1 147: 10 6->1 order: 1 147: 11 6->0 order: 1 147: 12 7->1 order: 1 147: 13 7->5 order: 1 147: 14 8->12 order: a conj?: 1 aromatic?: 1 147: 15 11->2 order: 1 stereo: CCW bonds: (9 4 5) conj?: 1 146: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 147: =============================================================================== 147: All tests passed (12742 assertions in 21 test cases) 147: 229/235 Test #147: distGeomHelpersCatch ................... Passed 127.77 sec 173: Query 3 171: =============================================================================== 171: All tests passed (93 assertions in 5 test cases) 171: 230/235 Test #171: testRascalCluster ...................... Passed 118.08 sec 146: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 173: Query 4 146: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 146: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 146: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 146: Nc1ncnc2c1ncn2[C@@H]1C[C@H](CO)[C@@H](O)C1 146: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 235: DbCLI/UnitTestDbCLI.py ............ [100%] 235: 235: =============================== warnings summary =============================== 235: ../obj-aarch64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20 235: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9) 235: decBase = declarative_base() 235: 235: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 235: ======================== 12 passed, 1 warning in 50.23s ======================== 231/235 Test #235: pythonProjectTests ..................... Passed 51.60 sec 146: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 146: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] 146: [15:25:39] Molecule does not have explicit Hs. Consider calling AddHs() 146: [15:25:33] --------------------------------- 146: [15:25:33] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system 146: [15:25:33] --------------------------------- 146: [15:25:33] More ChEMBL molecules failing bounds smoothing. 146: [15:25:33] --------------------------------- 146: [15:25:33] ugly conformations can be generated for highly constrained ring systems. 146: [15:25:33] --------------------------------- 146: [15:25:33] test embed parameters structure. 146: [15:25:33] --------------------------------- 146: [15:25:33] test github 1227: Hs being used in RMSD filtering. 146: [15:25:33] --------------------------------- 146: [15:25:33] Failure to embed larger aromatic rings. 146: [15:25:36] --------------------------------- 146: [15:25:36] Deterministic with large random seeds 146: [15:25:37] --------------------------------- 146: [15:25:37] Github #1990: seg fault after RemoveHs 146: [15:25:37] --------------------------------- 146: [15:25:37] Github #2246: Use coordMap when starting embedding from random coords 146: [15:25:39] --------------------------------- 146: [15:25:39] Providing a distance bounds matrix. 146: [15:25:39] --------------------------------- 146: [15:25:39] Disabling fragmentation. 146: [15:25:39] --------------------------------- 146: [15:25:39] Using symmetry in conformation pruning. 146: [15:25:39] --------------------------------- 146: [15:25:39] Force trans amides. 146: [15:25:39] --------------------------------- 146: [15:25:39] test missing Hs warning. 146: [15:25:39] --------------------------------- 146: [15:25:39] basic H bond support. 146: [15:25:39] ******************************************************* 232/235 Test #146: testDistGeomHelpers .................... Passed 139.61 sec 173: Query 5 170: =============================================================================== 170: All tests passed (3582 assertions in 34 test cases) 170: 233/235 Test #170: testRascalMCES ......................... Passed 133.15 sec 173: =============================================================================== 173: All tests passed (215 assertions in 18 test cases) 173: 234/235 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 148.91 sec 5: [15:41:31] Finished: testMultipleTimes() 5: [15:41:31] 5: ----------------------------------------- 235/235 Test #5: testConcurrentQueue .................... Passed 1108.67 sec 100% tests passed, 0 tests failed out of 235 Total Test time (real) = 1109.34 sec make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6' 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-202409.6' dh_auto_install cd obj-aarch64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/rdkit-202409.6/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202409.6 -B/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/spiral.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/retest.txt -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/listutils.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/fileutils.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemutils.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemdraw_qax.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemdraw.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/cactvs.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/utils.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/HTMLPiddler.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/testallps.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/pstests.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/pidtest.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/stringformat.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pid.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches/Imaging-1.1.1.diff -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pagesizes.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/formatted-strings.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/colors.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/pidWxDc.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/pidWX.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK/pidTK.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/pidSVG.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab/pidReportLab.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/README -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/pidQt4.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/pidQt.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/pidPyart.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/Fontmapping.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/psmetrics.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/pidPS.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/latin1MetricsCache.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/fontinfo.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-8.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-18.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-12.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-12.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-10.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-10.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/removemedium.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm -- Installing: 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Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pil -- Installing: 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Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesDupeFilter.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmartsRemover.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SDSupply.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/DbMolSupply.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Node.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Filter.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/TestRunner.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/SimilarityPickers.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDRandom.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDLogger.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDConfig.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/files.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring/Scoring.py -- Installing: 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-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_N15_pH74_netcharge1.pdb -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_JVE_pH74_netcharge1.pdb -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_AKI_pH74_netcharge1.pdb -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_ACP_pH74_netcharge1.pdb -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/crystal_aligned.pdb -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/aurka_protein_2c6e.pdb -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_renamed.pdb -- Installing: 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/build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Numerics/Conrec.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitForceField.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitForceField.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitForceField.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/Contrib.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/ForceField.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/AngleConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/AngleConstraints.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/DistanceConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/DistanceConstraints.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/PositionConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/TorsionConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/AngleBend.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/BondStretch.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/Contribs.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/DistanceConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/AngleConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/TorsionConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/PositionConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/Nonbonded.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/Params.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/Utils.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/Inversion.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/Inversions.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/TorsionAngle.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/AngleBend.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/BondStretch.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/StretchBend.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/OopBend.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/TorsionAngle.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/Nonbonded.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/Contribs.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/DistanceConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/AngleConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/TorsionConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/PositionConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/Params.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField/rdForceField.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDistGeometry.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDistGeometry.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDistGeometry.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/BoundsMatrix.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/ChiralSet.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/ChiralViolationContrib.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/ChiralViolationContribs.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/DistGeomUtils.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/DistViolationContrib.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/DistViolationContribs.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/FourthDimContrib.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/FourthDimContribs.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/TriangleSmooth.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DistanceGeometry/DistGeom.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitCatalogs.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitCatalogs.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitCatalogs.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Catalogs/CatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Catalogs/Catalog.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Catalogs/CatalogParams.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGraphMol.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGraphMol.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGraphMol.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Atom.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/atomic_data.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/AtomIterators.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Atropisomers.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Bond.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/BondIterators.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Canon.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Chirality.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Conformer.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/details.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/GraphMol.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolOps.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolPickler.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/PeriodicTable.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/QueryAtom.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/QueryBond.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/QueryOps.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RDKitBase.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RDKitQueries.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Resonance.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RingInfo.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Rings.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ROMol.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RWMol.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SanitException.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SubstanceGroup.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/StereoGroup.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MonomerInfo.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/new_canon.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolBundle.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSmilesParse.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSmilesParse.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSmilesParse.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmartsWrite.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParse.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParseOps.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesWrite.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/CanonicalizeStereoGroups.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDepictor.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDepictor.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDepictor.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Depictor/DepictUtils.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Depictor/EmbeddedFrag.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Depictor/RDDepictor.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdDepictor.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMarvinParser.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMarvinParser.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMarvinParser.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MarvinParse/MarvinParser.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFileParsers.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFileParsers.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFileParsers.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/CDXMLParser.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParsers.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParserUtils.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolFileStereochem.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileWriters.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolSupplier.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolSupplier.v1API.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolWriters.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceParsers.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceWriters.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/GeneralFileReader.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedSDMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/PNGParser.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubstructMatch.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructUtils.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGenericGroups.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGenericGroups.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGenericGroups.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/GenericGroups/GenericGroups.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemReactions.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemReactions.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemReactions.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Reaction.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionParser.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionPickler.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionFingerprints.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionUtils.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionRunner.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/PreprocessRxn.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/SanitizeRxn.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/Enumerate.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateBase.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/CartesianProduct.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSample.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdChemReactions.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemTransforms.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemTransforms.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemTransforms.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/ChemTransforms.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/MolFragmenter.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitTautomerQuery.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitTautomerQuery.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitTautomerQuery.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/TautomerQuery/TautomerQuery.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdTautomerQuery.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubgraphs.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubgraphs.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubgraphs.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Subgraphs/Subgraphs.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Subgraphs/SubgraphUtils.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFilterCatalog.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterCatalog.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterMatcherBase.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterMatchers.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdfiltercatalog.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFragCatalog.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFragCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFragCatalog.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatGenerator.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatParams.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragFPGenerator.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdfragcatalog.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDescriptors.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDescriptors.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDescriptors.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Crippen.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/BCUT.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Lipinski.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolDescriptors.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolSurf.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/ConnectivityDescriptors.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MQN.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/RegisterDescriptor.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Property.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AUTOCORR2D.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Data3Ddescriptors.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolData3Ddescriptors.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/USRDescriptor.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AtomFeat.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/OxidationNumbers.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/DCLV.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolDescriptors3D.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/EEM.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/PBF.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/PMI.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AUTOCORR3D.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/RDF.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MORSE.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/GETAWAY.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/WHIM.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/CoulombMat.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolDescriptors.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFingerprints.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFingerprints.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFingerprints.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/AtomPairs.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/Fingerprints.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MorganFingerprints.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MACCS.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MHFP.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/FingerprintGenerator.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/AtomPairGenerator.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MorganGenerator.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/RDKitFPGenerator.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/TopologicalTorsionGenerator.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/FingerprintUtil.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdFingerprintGenerator.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMHFPFingerprint.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitPartialCharges.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitPartialCharges.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitPartialCharges.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/PartialCharges/GasteigerCharges.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/PartialCharges/GasteigerParams.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdPartialCharges.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolTransforms.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolTransforms.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolTransforms.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolTransforms/MolTransforms.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolTransforms.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/FFConvenience.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/Builder.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/UFF.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/Builder.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/MMFF.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdForceFieldHelpers.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/DistGeomHelpers/Embedder.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdDistGeom.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolAlign.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolAlign.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolAlign.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitO3AAlign.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitO3AAlign.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitO3AAlign.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/AlignMolecules.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/O3AAlignMolecules.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolAlign.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/FeatureParser.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitShapeHelpers.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitShapeHelpers.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitShapeHelpers.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ShapeHelpers/ShapeEncoder.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ShapeHelpers/ShapeUtils.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdShapeHelpers.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolCatalog.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolCatalog.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalog.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolCatalog.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2D.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DSVG.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2Dwx.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DJS.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DUtils.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DHelpers.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolDraw2D.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolDraw2D.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolDraw2D.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DCairo.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/rdMolDraw2D.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFMCS.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFMCS.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFMCS.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FMCS/FMCS.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FMCS/Graph.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdFMCS.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolHash.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolHash.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolHash.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolHash/MolHash.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolHash/nmmolhash.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolHash.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMMPA.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMMPA.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMMPA.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MMPA/MMPA.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMMPA.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRascalMCES.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRascalMCES.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRascalMCES.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalMCES.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalOptions.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalClusterOptions.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalResult.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdRascalMCES.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSynthonSpaceSearch.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSynthonSpaceSearch.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSynthonSpaceSearch.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpace.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSet.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/Synthon.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SearchResults.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceSubstructureSearcher.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdSynthonSpaceSearch.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitCIPLabeler.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/CIPLabeler/CIPLabeler.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/CIPLabeler/TooManyNodesException.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdCIPLabeler.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDeprotect.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDeprotect.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDeprotect.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Deprotect/Deprotect.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdDeprotect.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitReducedGraphs.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ReducedGraphs/ReducedGraphs.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdReducedGraphs.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitTrajectory.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitTrajectory.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitTrajectory.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Snapshot.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Trajectory.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1 -- 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/build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RGroupDecomposition/RGroupDecomp.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RGroupDecomposition/RGroupDecompParams.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdRGroupDecomposition.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolInterchange.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolInterchange.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolInterchange.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolInterchange/MolInterchange.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolInterchange/details.h -- Installing: 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/build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/MolStandardize.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Metal.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Normalize.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Validate.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Charge.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Tautomer.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Fragment.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h -- Installing: 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/build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolEnumerator/LinkNode.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolEnumerator.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitAbbreviations.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitAbbreviations.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitAbbreviations.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Abbreviations/Abbreviations.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdAbbreviations.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 -- Installing: 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/build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/SetQuery.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/XOrQuery.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Features/Feature.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricFuncs.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricMatrixCalc.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip/Metric/rdMetricMatrixCalc.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSimDivPickers.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/SimDivPickers/DistPicker.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/SimDivPickers/LeaderPicker.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/SimDivPickers/HierarchicalClusterPicker.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/SimDivPickers/MaxMinPicker.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/rdSimDivPickers.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKithc.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKithc.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKithc.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Clustering.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitInfoTheory.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitInfoTheory.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitInfoTheory.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/rdInfoTheory.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/cQuantize.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1.2024.09.6 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1 -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ChemicalFeatures/ChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ChemicalFeatures/FreeChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdChemicalFeatures.so ===================================================================== PostgreSQL cartridge installation succeeded. ===================================================================== Restart the PostgreSQL service before using the PostgreSQL RDKit cartridge. ===================================================================== -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDPaths.py -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkit/rdkit-targets.cmake -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkit/rdkit-targets-none.cmake -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkit/rdkit-config.cmake -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkit/rdkit-config-version.cmake -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkitpython/rdkitpython-targets.cmake -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkitpython/rdkitpython-targets-none.cmake -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkitpython/rdkitpython-config.cmake -- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkitpython/rdkitpython-config-version.cmake make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/rdkit-202409.6' mkdir -p /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3 mv /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3/dist-packages rm -f -rf /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13 ln -sf /usr/share/fonts/truetype/freefont/FreeSans.ttf /build/reproducible-path/rdkit-202409.6/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-202409.6/debian/tmp/usr/lib/python3/dist-packages/rdkit/docs/ rm -f -rf /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/__pycache__ dh_numpy3 Possible precedence issue with control flow operator (return) at /usr/bin/dh_numpy3 line 57. Can't stat debian/librdkit1t64: No such file or directory at /usr/bin/dh_numpy3 line 85. dh_numpy3: warning: skipping binary package librdkit1t64 which does not depend on the NumPy C ABI Can't stat debian/librdkit-dev: No such file or directory at /usr/bin/dh_numpy3 line 85. dh_numpy3: warning: skipping binary package librdkit-dev which does not depend on the NumPy C ABI Can't stat debian/postgresql-17-rdkit: No such file or directory at /usr/bin/dh_numpy3 line 85. dh_numpy3: warning: skipping binary package postgresql-17-rdkit which does not depend on the NumPy C ABI dh_install for v in $(pg_buildext supported-versions); do \ mkdir -p debian/postgresql-$v-rdkit/usr/lib/postgresql/$v/lib/ debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \ cp Code/PgSQL/rdkit/build-$v/librdkit.so debian/postgresql-$v-rdkit/usr/lib/postgresql/$v/lib/rdkit.so; \ cp Code/PgSQL/rdkit/build-$v/rdkit*.sql debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \ cp Code/PgSQL/rdkit/build-$v/update_sql/rdkit*.sql debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \ cp Code/PgSQL/rdkit/rdkit.control debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \ done mkdir -p /build/reproducible-path/rdkit-202409.6/debian/rdkit-doc/usr/share/doc/rdkit/ # cp /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex/RDKit.pdf /build/reproducible-path/rdkit-202409.6/debian/rdkit-doc/usr/share/doc/rdkit/ cp -a /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/html /build/reproducible-path/rdkit-202409.6/debian/rdkit-doc/usr/share/doc/rdkit/ ln -sf /usr/share/javascript/jquery/jquery.js /build/reproducible-path/rdkit-202409.6/debian/rdkit-doc/usr/share/doc/rdkit//html/cppapi/jquery.js ln -sf /usr/share/javascript/jquery/jquery.js /build/reproducible-path/rdkit-202409.6/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/jquery.js ln -sf /usr/share/javascript/underscore/underscore.js /build/reproducible-path/rdkit-202409.6/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/underscore.js make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6' dh_installdocs -O--buildsystem=cmake debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/rdkit-202409.6' dh_installchangelogs ReleaseNotes.md make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6' debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/rdkit-202409.6' dh_python3 -ppython3-rdkit I: dh_python3 fs:421: renaming rdBase.so to rdBase.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdAbbreviations.so to rdAbbreviations.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdCIPLabeler.so to rdCIPLabeler.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdChemReactions.so to rdChemReactions.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdChemicalFeatures.so to rdChemicalFeatures.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdCoordGen.so to rdCoordGen.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdDepictor.so to rdDepictor.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdDeprotect.so to rdDeprotect.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdDistGeom.so to rdDistGeom.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdFMCS.so to rdFMCS.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdFingerprintGenerator.so to rdFingerprintGenerator.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdForceFieldHelpers.so to rdForceFieldHelpers.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdGeneralizedSubstruct.so to rdGeneralizedSubstruct.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMHFPFingerprint.so to rdMHFPFingerprint.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMIF.so to rdMIF.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMMPA.so to rdMMPA.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolAlign.so to rdMolAlign.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolCatalog.so to rdMolCatalog.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolChemicalFeatures.so to rdMolChemicalFeatures.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolDescriptors.so to rdMolDescriptors.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolEnumerator.so to rdMolEnumerator.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolHash.so to rdMolHash.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolInterchange.so to rdMolInterchange.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolProcessing.so to rdMolProcessing.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolTransforms.so to rdMolTransforms.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdPartialCharges.so to rdPartialCharges.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdRGroupDecomposition.so to rdRGroupDecomposition.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdRascalMCES.so to rdRascalMCES.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdReducedGraphs.so to rdReducedGraphs.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdSLNParse.so to rdSLNParse.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdShapeHelpers.so to rdShapeHelpers.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdSubstructLibrary.so to rdSubstructLibrary.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdSynthonSpaceSearch.so to rdSynthonSpaceSearch.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdTautomerQuery.so to rdTautomerQuery.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdchem.so to rdchem.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdfiltercatalog.so to rdfiltercatalog.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdfragcatalog.so to rdfragcatalog.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdinchi.so to rdinchi.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdmolfiles.so to rdmolfiles.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdmolops.so to rdmolops.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdqueries.so to rdqueries.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdtrajectory.so to rdtrajectory.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolDraw2D.so to rdMolDraw2D.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolStandardize.so to rdMolStandardize.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdScaffoldNetwork.so to rdScaffoldNetwork.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming cDataStructs.so to cDataStructs.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming DistGeom.so to DistGeom.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdForceField.so to rdForceField.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdGeometry.so to rdGeometry.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming Clustering.so to Clustering.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming cQuantize.so to cQuantize.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdInfoTheory.so to rdInfoTheory.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdAlignment.so to rdAlignment.cpython-313-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-313-aarch64-linux-gnu.so dh_numpy3 -ppython3-rdkit Possible precedence issue with control flow operator (return) at /usr/bin/dh_numpy3 line 57. make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6' 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-202409.6' dh_missing --list-missing dh_missing: warning: usr/lib/postgresql/17/lib/rdkit.so exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_Correlation.csv exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_CorrMat.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_Correlation.csv exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/README exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/ForceField/ForceFieldTerms.new.odt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/ForceField/UFF Parameters.ods exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/BackwardsIncompatibleChanges.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/CMakeLists.txt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/FindMyRDKit.cmake exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example1.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example10.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example11.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example12.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example13.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example14.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example15.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example16.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example17.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example2.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example3.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example4.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example5.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example6.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example7.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example8.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example9.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/Cartridge.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/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/GettingStartedWithContributing.md 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: 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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.md 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/gen_rdkit_stubs/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/gen_rdkit_stubs/__main__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/gen_rdkit_stubs/worker.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/patch_rdkit_docstrings/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/patch_rdkit_docstrings/__main__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/patch_rdkit_docstrings/clang_worker.py 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 dh_missing: warning: usr/share/postgresql/17/extension/rdkit--3.8--4.0.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.0--4.0.1.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.0.1--4.1.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.1--4.1.1.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.1.1--4.2.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.2--4.3.0.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.3.0--4.4.0.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.4.0--4.5.0.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.5.0--4.6.0.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.6.0--4.6.1.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.6.1.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit.control 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 (64), librdkit1t64 (124), postgresql-17-rdkit (0), python3-rdkit (1), rdkit-data (3), rdkit-doc (0) * dh_installdocs: librdkit-dev (0), librdkit1t64 (0), postgresql-17-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-202409.6' dh_dwz -a -O--buildsystem=cmake dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol errfinish: it's probably a plugin dpkg-shlibdeps: warning: 24 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_ValueError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetObject used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries dpkg-shlibdeps: warning: 2 other similar warnings have been skipped (use -v to see them all) dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: 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: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202409.6-2_arm64.deb'. dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202409.6-2_arm64.deb'. dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202409.6-2_all.deb'. dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202409.6-2_arm64.deb'. dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202409.6-2_all.deb'. dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202409.6-2_arm64.deb'. dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202409.6-2_arm64.deb'. dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202409.6-2_arm64.deb'. dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202409.6-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202409.6-2_arm64.buildinfo dpkg-genchanges --build=binary -O../rdkit_202409.6-2_arm64.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: user script /srv/workspace/pbuilder/2068256/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2068256/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2068256 and its subdirectories I: Current time: Sun Apr 12 15:50:17 +14 2026 I: pbuilder-time-stamp: 1775958617