Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/r/rdkit/rdkit_202203.2-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/rdkit-202203.2-1v9omh7v5/rdkit_202203.2-1_amd64.buildinfo Get source package info: rdkit=202203.2-1 Source URL: http://snapshot.notset.fr/mr/package/rdkit/202203.2-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.121 autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-6 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6 binutils=2.38-3 binutils-common=2.38-3 binutils-x86-64-linux-gnu=2.38-3 bison=2:3.8.2+dfsg-1 bsdextrautils=2.38-4 bsdutils=1:2.38-4 build-essential=12.9 bzip2=1.0.8-5 ca-certificates=20211016 catch2=2.13.9-1 clang-13=1:13.0.1-3+b2 cmake=3.23.1-2 cmake-data=3.23.1-2 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.3.0-1 dash=0.5.11+git20210903+057cd650a4ed-8 debconf=1.5.79 debhelper=13.7.1 debianutils=5.7-0.1 dh-autoreconf=20 dh-elpa-helper=2.0.10 dh-python=5.20220403 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 docutils-common=0.17.1+dfsg-2 doxygen=1.9.1-2 dpkg=1.21.7 dpkg-dev=1.21.7 dwz=0.14-1 emacsen-common=3.0.4 file=1:5.41-4 findutils=4.9.0-3 flex=2.6.4-8 fontconfig=2.13.1-4.4 fontconfig-config=2.13.1-4.4 fonts-dejavu-core=2.37-2 fonts-lmodern=2.005-1 g++=4:11.2.0-2 g++-11=11.3.0-1 gcc=4:11.2.0-2 gcc-11=11.3.0-1 gcc-11-base=11.3.0-1 gcc-12-base=12-20220319-1 gettext=0.21-6 gettext-base=0.21-6 grep=3.7-1 groff-base=1.22.4-8 gzip=1.12-1 hicolor-icon-theme=0.17-2 hostname=3.23 icu-devtools=71.1-2 imagemagick=8:6.9.11.60+dfsg-1.3+b2 imagemagick-6-common=8:6.9.11.60+dfsg-1.3 imagemagick-6.q16=8:6.9.11.60+dfsg-1.3+b2 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 latexmk=1:4.77-1 lib32gcc-s1=12-20220319-1 lib32stdc++6=12-20220319-1 libacl1=2.3.1-1 libaom3=3.3.0-1 libapache-pom-java=18-1 libarchive-zip-perl=1.68-1 libarchive13=3.6.0-1 libasan6=11.3.0-1 libatomic1=12-20220319-1 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libbinutils=2.38-3 libblas3=3.10.1-1 libblkid-dev=2.38-4 libblkid1=2.38-4 libboost-atomic1.74-dev=1.74.0-14+b1 libboost-atomic1.74.0=1.74.0-14+b1 libboost-chrono1.74-dev=1.74.0-14+b1 libboost-chrono1.74.0=1.74.0-14+b1 libboost-date-time1.74-dev=1.74.0-14+b1 libboost-date-time1.74.0=1.74.0-14+b1 libboost-dev=1.74.0.3 libboost-iostreams-dev=1.74.0.3 libboost-iostreams1.74-dev=1.74.0-14+b1 libboost-iostreams1.74.0=1.74.0-14+b1 libboost-python-dev=1.74.0.3 libboost-python1.74-dev=1.74.0-14+b1 libboost-python1.74.0=1.74.0-14+b1 libboost-regex-dev=1.74.0.3 libboost-regex1.74-dev=1.74.0-14+b1 libboost-regex1.74.0=1.74.0-14+b1 libboost-serialization1.74-dev=1.74.0-14+b1 libboost-serialization1.74.0=1.74.0-14+b1 libboost-system-dev=1.74.0.3 libboost-system1.74-dev=1.74.0-14+b1 libboost-system1.74.0=1.74.0-14+b1 libboost-thread-dev=1.74.0.3 libboost-thread1.74-dev=1.74.0-14+b1 libboost-thread1.74.0=1.74.0-14+b1 libboost1.74-dev=1.74.0-14+b1 libbrotli-dev=1.0.9-2+b3 libbrotli1=1.0.9-2+b3 libbsd0=0.11.6-1 libbz2-1.0=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libc6-i386=2.33-7 libcairo-gobject2=1.16.0-5 libcairo-script-interpreter2=1.16.0-5 libcairo2=1.16.0-5 libcairo2-dev=1.16.0-5 libcap-ng0=0.7.9-2.2+b2 libcap2=1:2.44-1 libcc1-0=12-20220319-1 libclang-common-13-dev=1:13.0.1-3+b2 libclang-cpp11=1:11.1.0-6+b2 libclang-cpp13=1:13.0.1-3+b2 libclang1-11=1:11.1.0-6+b2 libclang1-13=1:13.0.1-3+b2 libcmark-gfm-extensions0.29.0.gfm.3=0.29.0.gfm.3-3+b1 libcmark-gfm0.29.0.gfm.3=0.29.0.gfm.3-3+b1 libcom-err2=1.46.5-2 libcommons-logging-java=1.2-3 libcommons-parent-java=43-1 libcoordgen-dev=3.0.0-2 libcoordgen3=3.0.0-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-3 libctf0=2.38-3 libcurl4=7.82.0-2 libdatrie1=0.2.13-2 libdav1d5=0.9.2-1+b1 libdb5.3=5.3.28+dfsg1-0.8 libde265-0=1.0.8-1 libdebconfclient0=0.262 libdebhelper-perl=13.7.1 libdeflate0=1.10-2 libdpkg-perl=1.21.7 libedit2=3.1-20210910-1 libeigen3-dev=3.4.0-2 libelf1=0.186-1 libexpat1=2.4.8-1 libexpat1-dev=2.4.8-1 libffi-dev=3.4.2-4 libffi8=3.4.2-4 libfftw3-double3=3.3.8-2 libfile-stripnondeterminism-perl=1.13.0-1 libfontbox-java=1:1.8.16-2 libfontconfig-dev=2.13.1-4.4 libfontconfig1=2.13.1-4.4 libfontconfig1-dev=2.13.1-4.4 libfontenc1=1:1.1.4-1 libfreetype-dev=2.11.1+dfsg-2 libfreetype6=2.11.1+dfsg-2 libfreetype6-dev=2.11.1+dfsg-2 libfribidi0=1.0.8-2.1 libgc1=1:8.0.6-1.1 libgcc-11-dev=11.3.0-1 libgcc-s1=12-20220319-1 libgcrypt20=1.10.1-2 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgdk-pixbuf-2.0-0=2.42.8+dfsg-1 libgdk-pixbuf2.0-common=2.42.8+dfsg-1 libgfortran5=12-20220319-1 libglib2.0-0=2.72.1-1 libglib2.0-bin=2.72.1-1 libglib2.0-data=2.72.1-1 libglib2.0-dev=2.72.1-1 libglib2.0-dev-bin=2.72.1-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.4-2 libgomp1=12-20220319-1 libgpg-error0=1.43-3 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.19.2-2+b1 libharfbuzz0b=2.7.4-1+b1 libheif1=1.12.0-2+b3 libhogweed6=3.7.3-1 libice-dev=2:1.0.10-1 libice6=2:1.0.10-1 libicu-dev=71.1-2 libicu71=71.1-2 libidn2-0=2.3.2-2 libimagequant0=2.17.0-1 libisl23=0.24-2 libitm1=12-20220319-1 libjbig0=2.1-3.1+b2 libjpeg62-turbo=1:2.1.2-1 libjs-jquery=3.6.0+dfsg+~3.5.13-1 libjs-sphinxdoc=4.5.0-3 libjs-underscore=1.13.3~dfsg+~1.11.4-1 libjson-perl=4.04000-1 libjsoncpp25=1.9.5-4 libk5crypto3=1.19.2-2+b1 libkeyutils1=1.6.1-3 libkpathsea6=2021.20210626.59705-1+b1 libkrb5-3=1.19.2-2+b1 libkrb5support0=1.19.2-2+b1 liblapack3=3.10.1-1 liblcms2-2=2.12~rc1-2 libldap-2.5-0=2.5.11+dfsg-1 libllvm11=1:11.1.0-6+b2 libllvm13=1:13.0.1-3+b2 liblqr-1-0=0.4.2-2.1 liblsan0=12-20220319-1 libltdl7=2.4.7-3 liblz4-1=1.9.3-2 liblzma5=5.2.5-2.1 liblzo2-2=2.10-2 libmaeparser-dev=1.2.4-1+b1 libmaeparser1=1.2.4-1+b1 libmagic-mgc=1:5.41-4 libmagic1=1:5.41-4 libmagickcore-6.q16-6=8:6.9.11.60+dfsg-1.3+b2 libmagickwand-6.q16-6=8:6.9.11.60+dfsg-1.3+b2 libmd0=1.0.4-1 libmount-dev=2.38-4 libmount1=2.38-4 libmpc3=1.2.1-2 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncurses-dev=6.3+20220423-1 libncurses6=6.3+20220423-1 libncursesw6=6.3+20220423-1 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnuma1=2.0.14-3 libobjc-11-dev=11.3.0-1 libobjc4=12-20220319-1 libopenjp2-7=2.4.0-6 libp11-kit0=0.24.1-1 libpam-modules=1.4.0-11 libpam-modules-bin=1.4.0-11 libpam-runtime=1.4.0-11 libpam0g=1.4.0-11 libpango-1.0-0=1.50.6+ds-2 libpangocairo-1.0-0=1.50.6+ds-2 libpangoft2-1.0-0=1.50.6+ds-2 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libpcre16-3=2:8.39-14 libpcre2-16-0=10.40-1 libpcre2-32-0=10.40-1 libpcre2-8-0=10.40-1 libpcre2-dev=10.40-1 libpcre2-posix3=10.40-1 libpcre3=2:8.39-14 libpcre3-dev=2:8.39-14 libpcre32-3=2:8.39-14 libpcrecpp0v5=2:8.39-14 libpdfbox-java=1:1.8.16-2 libperl5.34=5.34.0-4 libpfm4=4.11.1+git32-gd0b85fb-1 libpipeline1=1.5.6-1 libpixman-1-0=0.40.0-1 libpixman-1-dev=0.40.0-1 libpng-dev=1.6.37-5 libpng16-16=1.6.37-5 libpq-dev=14.2-1+b3 libpq5=14.2-1+b3 libprocps8=2:3.3.17-7+b1 libpsl5=0.21.0-1.2 libptexenc1=2021.20210626.59705-1+b1 libpthread-stubs0-dev=0.4-1 libpython3-dev=3.10.4-1 libpython3-stdlib=3.10.4-1 libpython3.10=3.10.4-3 libpython3.10-dev=3.10.4-3 libpython3.10-minimal=3.10.4-3 libpython3.10-stdlib=3.10.4-3 libpython3.9-minimal=3.9.12-1 libpython3.9-stdlib=3.9.12-1 libquadmath0=12-20220319-1 libraqm0=0.7.0-4 libreadline8=8.1.2-1.2 librhash0=1.4.2-1 librsvg2-2=2.52.5+dfsg-3+b1 librsvg2-bin=2.52.5+dfsg-3+b1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.28+dfsg-4 libsasl2-modules-db=2.1.28+dfsg-4 libseccomp2=2.5.4-1 libselinux1=3.3-1+b2 libselinux1-dev=3.3-1+b2 libsemanage-common=3.3-1 libsemanage2=3.3-1+b2 libsepol-dev=3.3-1 libsepol2=3.3-1 libsigsegv2=2.14-1 libsm-dev=2:1.2.3-1 libsm6=2:1.2.3-1 libsmartcols1=2.38-4 libsqlite3-0=3.38.2-1 libsqlite3-dev=3.38.2-1 libssh2-1=1.10.0-3 libssl-dev=1.1.1n-1 libssl1.1=1.1.1n-1 libstdc++-11-dev=11.3.0-1 libstdc++6=12-20220319-1 libsub-override-perl=0.09-2 libsynctex2=2021.20210626.59705-1+b1 libsystemd0=250.4-1 libtasn1-6=4.18.0-4 libteckit0=2.5.11+ds1-1 libtexlua53=2021.20210626.59705-1+b1 libtexluajit2=2021.20210626.59705-1+b1 libthai-data=0.1.29-1 libthai0=0.1.29-1 libtiff5=4.3.0-7 libtinfo-dev=6.3+20220423-1 libtinfo6=6.3+20220423-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.7-3 libtsan0=11.3.0-1 libubsan1=12-20220319-1 libuchardet0=0.0.7-1 libudev1=250.4-1 libunicode-escape-perl=0.0.2-4.1 libunicode-string-perl=2.10-1+b7 libunistring2=1.0-1 libuuid1=2.38-4 libuv1=1.44.1-2 libwebp7=1.2.2-2+b1 libwebpdemux2=1.2.2-2+b1 libwebpmux3=1.2.2-2+b1 libx11-6=2:1.7.5-1 libx11-data=2:1.7.5-1 libx11-dev=2:1.7.5-1 libx265-199=3.5-2 libxapian30=1.4.18-4 libxau-dev=1:1.0.9-1 libxau6=1:1.0.9-1 libxaw7=2:1.0.14-1 libxcb-render0=1.14-3 libxcb-render0-dev=1.14-3 libxcb-shm0=1.14-3 libxcb-shm0-dev=1.14-3 libxcb1=1.14-3 libxcb1-dev=1.14-3 libxdmcp-dev=1:1.1.2-3 libxdmcp6=1:1.1.2-3 libxext-dev=2:1.3.4-1 libxext6=2:1.3.4-1 libxi6=2:1.8-1 libxml2=2.9.13+dfsg-1+b1 libxml2-dev=2.9.13+dfsg-1+b1 libxmu6=2:1.1.3-3 libxpm4=1:3.5.12-1 libxrender-dev=1:0.9.10-1 libxrender1=1:0.9.10-1 libxt6=1:1.2.1-1 libyaml-0-2=0.2.2-1 libz3-4=4.8.12-1+b1 libz3-dev=4.8.12-1+b1 libzstd1=1.5.2+dfsg-1 libzzip-0-13=0.13.72+dfsg.1-1.1 linux-libc-dev=5.17.3-1 llvm-13=1:13.0.1-3+b2 llvm-13-dev=1:13.0.1-3+b2 llvm-13-linker-tools=1:13.0.1-3+b2 llvm-13-runtime=1:13.0.1-3+b2 llvm-13-tools=1:13.0.1-3+b2 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 m4=1.4.18-5 mailcap=3.70+nmu1 make=4.3-4.1 man-db=2.10.2-1 mawk=1.3.4.20200120-3+b1 media-types=7.1.0 mime-support=3.66 ncurses-base=6.3-2 ncurses-bin=6.3-2 netbase=6.3 openssl=1.1.1n-1 pandoc=2.9.2.1-3+b2 pandoc-data=2.9.2.1-3 passwd=1:4.11.1+dfsg1-2 patch=2.7.6-7 perl=5.34.0-4 perl-base=5.34.0-4 perl-modules-5.34=5.34.0-4 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 postgresql-client-14=14.2-1+b3 postgresql-client-common=240 postgresql-common=240 postgresql-server-dev-14=14.2-1+b3 postgresql-server-dev-all=240 preview-latex-style=12.2-1 procps=2:3.3.17-7+b1 python-babel-localedata=2.8.0+dfsg.1-7 python3=3.10.4-1 python3-alabaster=0.7.12-1 python3-babel=2.8.0+dfsg.1-7 python3-certifi=2020.6.20-1 python3-chardet=4.0.0-2 python3-charset-normalizer=2.0.6-2 python3-commonmark=0.9.1-4 python3-dateutil=2.8.1-6 python3-dev=3.10.4-1 python3-distutils=3.9.12-1 python3-docutils=0.17.1+dfsg-2 python3-greenlet=1.1.2-3+b1 python3-idna=3.3-1 python3-imagesize=1.3.0-1 python3-importlib-metadata=4.6.4-1 python3-jinja2=3.0.3-1 python3-lib2to3=3.9.12-1 python3-markupsafe=2.0.1-2+b1 python3-minimal=3.10.4-1 python3-more-itertools=8.10.0-2 python3-numpy=1:1.21.5-1 python3-packaging=21.3-1 python3-pandas=1.3.5+dfsg-4 python3-pandas-lib=1.3.5+dfsg-4 python3-pil=9.1.0-1 python3-pkg-resources=59.6.0-1.2 python3-pygments=2.11.2+dfsg-2 python3-pyparsing=3.0.7-2 python3-recommonmark=0.6.0+ds-1 python3-requests=2.27.1+dfsg-1 python3-roman=3.3-1 python3-six=1.16.0-3 python3-snowballstemmer=2.2.0-1 python3-sphinx=4.5.0-3 python3-sqlalchemy=1.4.31+ds1-1 python3-tz=2022.1-1 python3-urllib3=1.26.9-1 python3-yaml=5.4.1-1+b1 python3-zipp=1.0.0-3 python3.10=3.10.4-3 python3.10-dev=3.10.4-3 python3.10-minimal=3.10.4-3 python3.9=3.9.12-1 python3.9-minimal=3.9.12-1 rapidjson-dev=1.1.0+dfsg2-7 readline-common=8.1.2-1.2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sgml-base=1.30 shared-mime-info=2.1-2 sphinx-common=4.5.0-3 ssl-cert=1.1.2 sysvinit-utils=3.03-1 t1utils=1.41-4 tar=1.34+dfsg-1 tex-common=6.17 tex-gyre=20180621-3.1 texlive-base=2021.20220204-1 texlive-binaries=2021.20210626.59705-1+b1 texlive-fonts-recommended=2021.20220204-1 texlive-latex-base=2021.20220204-1 texlive-latex-extra=2021.20220204-1 texlive-latex-recommended=2021.20220204-1 texlive-pictures=2021.20220204-1 tzdata=2022a-1 ucf=3.0043 util-linux=2.38-4 util-linux-extra=2.38-4 uuid-dev=2.38-4 x11-common=1:7.7+23 x11proto-dev=2022.1-1 xdg-utils=1.1.3-4.1 xfonts-encodings=1:1.0.4-2.1 xfonts-utils=1:7.7+6 xml-core=0.18+nmu1 xorg-sgml-doctools=1:1.11-1.1 xtrans-dev=1.4.0-1 xz-utils=5.2.5-2.1 zlib1g=1:1.2.11.dfsg-4 zlib1g-dev=1:1.2.11.dfsg-4 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220427T153344Z/ unstable main deb-src http://snapshot.notset.fr/archive/debian/20220427T153344Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220430T085917Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220425T152932Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d rdkit=202203.2-1 && mkdir -p /build/rdkit-8H2dlr && dpkg-source --no-check -x /*.dsc /build/rdkit-8H2dlr/rdkit-202203.2 && chown -R builduser:builduser /build/rdkit-8H2dlr" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/rdkit-8H2dlr/rdkit-202203.2 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1651049389" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/rdkit-8H2dlr /tmp/rdkit-202203.2-1v9omh7v5 bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220425T152932Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.t0nfn1mFkO as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.t0nfn1mFkO Reading package lists... Building dependency tree... util-linux is already the newest version (2.38-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220425T152932Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220425T152932Z unstable/main amd64 fakeroot amd64 1.28-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (1102 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4702 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.28-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.28-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.28-1_amd64.deb ... Unpacking fakeroot (1.28-1) ... Setting up libfakeroot:amd64 (1.28-1) ... Setting up fakeroot (1.28-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220427T153344Z/ unstable main deb-src http://snapshot.notset.fr/archive/debian/20220427T153344Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220430T085917Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220425T152932Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.t0nfn1mFkO Get:1 http://snapshot.notset.fr/archive/debian/20220427T153344Z unstable InRelease [165 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220430T085917Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20220425T152932Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20220427T153344Z unstable/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220427T153344Z unstable/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220427T153344Z unstable/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220427T153344Z unstable/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220427T153344Z unstable/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220427T153344Z unstable/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20220427T153344Z unstable/main Sources [12.9 MB] Get:5 http://snapshot.notset.fr/archive/debian/20220427T153344Z unstable/main amd64 Packages [12.4 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20220430T085917Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20220430T085917Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20220430T085917Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20220430T085917Z unstable/main amd64 Packages [12.4 MB] Fetched 38.0 MB in 31s (1236 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.t0nfn1mFkO I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d rdkit=202203.2-1 && mkdir -p /build/rdkit-8H2dlr && dpkg-source --no-check -x /*.dsc /build/rdkit-8H2dlr/rdkit-202203.2 && chown -R builduser:builduser /build/rdkit-8H2dlr"' exec /tmp/mmdebstrap.t0nfn1mFkO Reading package lists... NOTICE: 'rdkit' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/rdkit.git Please use: git clone https://salsa.debian.org/debichem-team/rdkit.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 60.9 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220427T153344Z unstable/main rdkit 202203.2-1 (dsc) [2845 B] Get:2 http://snapshot.notset.fr/archive/debian/20220427T153344Z unstable/main rdkit 202203.2-1 (tar) [60.8 MB] Get:3 http://snapshot.notset.fr/archive/debian/20220427T153344Z unstable/main rdkit 202203.2-1 (diff) [101 kB] Fetched 60.9 MB in 47s (1296 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'rdkit_202203.2-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting rdkit in /build/rdkit-8H2dlr/rdkit-202203.2 dpkg-source: info: unpacking rdkit_202203.2.orig.tar.xz dpkg-source: info: unpacking rdkit_202203.2-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying NoDownloads.patch dpkg-source: info: applying postgres_Makefile_fixes.patch dpkg-source: info: applying sphinx_imgconverter.patch dpkg-source: info: applying catch2_header.patch dpkg-source: info: applying postgres_alternative_test_outputs.patch dpkg-source: info: applying postgres_compile_fixes.patch dpkg-source: info: applying sphinx_compile_fixes.patch dpkg-source: info: applying extra_float_digits I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/rdkit-8H2dlr/rdkit-202203.2 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1651049389" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.t0nfn1mFkO dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202203.2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Christoph Berg dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean pg_buildext checkcontrol dh clean --with python3 --buildsystem=cmake --parallel dh: warning: Compatibility levels before 10 are deprecated (level 9 in use) debian/rules override_dh_auto_clean make[1]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2' find /build/rdkit-8H2dlr/rdkit-202203.2 -name "*.pyc" | xargs rm -f rm -f -r Projects/DbCLI/testData/bzr/ rdkit/Chem/inchi.py rm -f -r Docs/Book/_build Code/docs rdkit/docs Code/doxygen_sqlite3.db rm -f \ Code/ForceField/MMFF/test_data/MMFF94_dative_min.sdf \ Code/ForceField/MMFF/test_data/MMFF94_dative_min_from_SMILES.sdf \ Code/ForceField/MMFF/test_data/MMFF94_hypervalent_min.sdf \ Code/ForceField/MMFF/test_data/MMFF94_hypervalent_min_from_SMILES.sdf \ Code/ForceField/MMFF/test_data/MMFF94_reference.log \ Code/ForceField/MMFF/test_data/MMFF94s_reference.log \ Code/ForceField/MMFF/test_data/testMMFFForceField.log \ Code/GraphMol/Depictor/test_data/cis_trans_cpp.out.sdf \ Code/GraphMol/Depictor/test_data/collisions.out.sdf \ Code/GraphMol/Depictor/test_data/first_200.out.sdf \ Code/GraphMol/Depictor/test_data/test1.out.sdf \ Code/GraphMol/FileParsers/test_data/blah.sdf \ Code/GraphMol/FileParsers/test_data/cdk2_stereo.sdf \ Code/GraphMol/FileParsers/test_data/outNCI_few.sdf \ Code/GraphMol/FileParsers/test_data/outNCI_few.tdt \ Code/GraphMol/FileParsers/test_data/outNCI_first_200.props.sdf \ Code/GraphMol/FileParsers/test_data/outSmiles.csv \ Code/GraphMol/ForceFieldHelpers/UFF/test_data/Issue62.sdf \ Code/GraphMol/MolAlign/test_data/ref_e2_pyCrippenO3A.sdf \ Code/GraphMol/SLNParse/lex.yysln.cpp \ Code/GraphMol/SLNParse/sln.tab.cpp \ Code/GraphMol/SLNParse/sln.tab.hpp \ Code/GraphMol/SmilesParse/lex.yysmarts.cpp \ Code/GraphMol/SmilesParse/lex.yysmiles.cpp \ Code/GraphMol/SmilesParse/smarts.tab.cpp \ Code/GraphMol/SmilesParse/smarts.tab.hpp \ Code/GraphMol/SmilesParse/smiles.tab.cpp \ Code/GraphMol/SmilesParse/smiles.tab.hpp \ Code/GraphMol/Wrap/test_data/outNCI_few.sdf \ Code/GraphMol/Wrap/test_data/outSmiles.txt \ Code/RDGeneral/versions.cpp \ Docs/Book/Cartridge.rst \ Docs/Book/Cookbook.rst \ Docs/Book/Install.rst \ Docs/Book/Overview.rst \ rdkit/ML/Data/test_data/testgeneral.dat.pkl \ rdkit/ML/Data/test_data/testquant.qdat.pkl rm -f Code/RDGeneral/versions.h rdkit/sping/tests/testallps.ps dh_auto_clean dh_auto_clean: warning: Compatibility levels before 10 are deprecated (level 9 in use) pg_buildext clean /build/rdkit-8H2dlr/rdkit-202203.2/Code/PgSQL/rdkit build-%v rm -rf build-*/ make[1]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2' dh_clean -O--buildsystem=cmake -O--parallel dh_clean: warning: Compatibility levels before 10 are deprecated (level 9 in use) debian/rules build-arch dh build-arch --with python3 --buildsystem=cmake --parallel dh: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_update_autotools_config -a -O--buildsystem=cmake -O--parallel debian/rules override_dh_auto_configure make[1]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2' dh_auto_configure -- -DCMAKE_BUILD_TYPE=None -DCMAKE_SKIP_RPATH=ON -DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_THREADSAFE_SSS=ON -DRDK_BUILD_PYTHON_WRAPPERS=ON -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_USE_URF=OFF -DRDK_INSTALL_COMIC_FONTS=OFF -DRDK_BUILD_CAIRO_SUPPORT=ON -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=/usr -DCATCH_DIR=/usr/include/catch2 -DPYTHON_EXECUTABLE=/usr/bin/python3.10 ../ dh_auto_configure: warning: Compatibility levels before 10 are deprecated (level 9 in use) cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCMAKE_BUILD_TYPE=None -DCMAKE_SKIP_RPATH=ON -DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_THREADSAFE_SSS=ON -DRDK_BUILD_PYTHON_WRAPPERS=ON -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_USE_URF=OFF -DRDK_INSTALL_COMIC_FONTS=OFF -DRDK_BUILD_CAIRO_SUPPORT=ON -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=/usr -DCATCH_DIR=/usr/include/catch2 -DPYTHON_EXECUTABLE=/usr/bin/python3.10 ../ .. -- The C compiler identification is GNU 11.3.0 -- The CXX compiler identification is GNU 11.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Catch2: /usr/include/catch2 CATCH: /usr/include/catch2 -- Found PythonInterp: /usr/bin/python3.10 (found version "3.10.4") -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.10.so (found version "3.10.4") :1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives :1: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead CMake Warning at /usr/share/cmake-3.23/Modules/FindBoost.cmake:2216 (message): No header defined for python-py310; skipping header check (note: header-only libraries have no designated component) Call Stack (most recent call first): CMakeLists.txt:292 (find_package) :1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives :1: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead Python Install directory /usr/lib/python3/dist-packages :1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives :1: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead PYTHON Py_ENABLE_SHARED: 1 PYTHON USING LINK LINE: -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 nbval not found, disabling the jupyter tests -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.58.0") found components: system serialization iostreams regex == Using strict rotor definition -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.58.0") found components: system iostreams regex -- maeparser include dir set as '/usr/include' -- maeparser libraries set as '/usr/lib/x86_64-linux-gnu/libmaeparser.so' -- Found maeparser: /usr/include -- coordgen include dir set as /usr/include -- coordgen libraries set as '/usr/lib/x86_64-linux-gnu/libcoordgen.so' -- Found coordgen: /usr/include -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.58.0") found components: iostreams regex -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.58.0") found components: system iostreams regex -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") == Updating Filters.cpp from pains file == Done updating pains files -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- Found Cairo: /usr/include/cairo -- Found Freetype: /usr/lib/x86_64-linux-gnu/libfreetype.so (found version "2.11.1") -- Could NOT find Boost (missing: program_options) (found suitable version "1.74.0", minimum required is "1.58.0") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2' debian/rules override_dh_auto_build make[1]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2' dh_auto_build dh_auto_build: warning: Compatibility levels before 10 are deprecated (level 9 in use) cd obj-x86_64-linux-gnu && make -j10 VERBOSE=1 make[2]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/rdkit-8H2dlr/rdkit-202203.2 -B/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/CMakeFiles /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.dir/depend make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/depend make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/External/catch /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/External/catch /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/External/catch/CMakeFiles/catch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/External/INCHI-API /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/External/INCHI-API /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake --color= make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/depend make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/External/CoordGen /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/External/CoordGen /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/DependInfo.cmake --color= make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDGeneral /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDGeneral /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake --color= make -f 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/build/rdkit-8H2dlr/rdkit-202203.2/External/GA/ga/StringChromosome.cpp [ 2%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/External/GA/ga/Chromosome.cpp [ 2%] Linking C shared library ../../../../lib/libRDKithc.so cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKithc.so.1 -o ../../../../lib/libRDKithc.so.1.2022.03.2 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o -lpthread cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2022.03.2 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 2%] Built target hc [ 3%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/External/GA/ga/IntegerStringChromosomePolicy.cpp [ 3%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 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-MT External/GA/CMakeFiles/ga.dir/util/Util.cpp.o -MF CMakeFiles/ga.dir/util/Util.cpp.o.d -o CMakeFiles/ga.dir/util/Util.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/External/GA/util/Util.cpp /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDGeneral/RDLog.cpp: In function ‘std::ostream& RDLog::toStream(std::ostream&)’: /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDGeneral/RDLog.cpp:155:14: warning: unused variable ‘tm’ [-Wunused-variable] 155 | struct tm *tm; | ^~ [ 3%] Linking CXX shared library ../../lib/libRDKitga.so cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitga.so.1 -o ../../lib/libRDKitga.so.1.2022.03.2 CMakeFiles/ga.dir/ga/StringChromosome.cpp.o CMakeFiles/ga.dir/ga/Chromosome.cpp.o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/util/RandomUtil.cpp.o CMakeFiles/ga.dir/util/Util.cpp.o -lpthread cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitga.so.1.2022.03.2 ../../lib/libRDKitga.so.1 ../../lib/libRDKitga.so make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 3%] Built target ga [ 3%] Linking CXX shared library ../../lib/libRDKitRDStreams.so cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDStreams.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat 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-g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o ../../lib/libRDKitRDGeneral.so.1.2022.03.2 CMakeFiles/RDGeneral.dir/Invariant.cpp.o CMakeFiles/RDGeneral.dir/types.cpp.o CMakeFiles/RDGeneral.dir/utils.cpp.o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o CMakeFiles/RDGeneral.dir/RDLog.cpp.o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o CMakeFiles/RDGeneral.dir/versions.cpp.o -ldl -lpthread cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeneral.so.1.2022.03.2 ../../lib/libRDKitRDGeneral.so.1 ../../lib/libRDKitRDGeneral.so make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 3%] Built target RDGeneral make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/Code/DataStructs /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --color= make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd 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--color= make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDGeneral /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDGeneral /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDGeneral /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDGeneral /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake --color= make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/depend make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDGeneral /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDGeneral 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directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDGeneral /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDGeneral /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/logTestsCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT 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Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT 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-Wextra -fPIC -std=gnu++14 -MD -MT Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -MF CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o.d -o CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDGeneral/catch_dict.cpp [ 3%] Building CXX object Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++14 -MD -MT Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o -MF CMakeFiles/testRDValue.dir/testRDValue.cpp.o.d -o CMakeFiles/testRDValue.dir/testRDValue.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDGeneral/testRDValue.cpp make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 3%] Building CXX object Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/catch2 -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++14 -MD -MT Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -MF CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o.d -o CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDGeneral/catch_logs.cpp make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 3%] Building CXX object Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDGeneral && 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/build/rdkit-8H2dlr/rdkit-202203.2/Code/RDGeneral/testConcurrentQueue.cpp make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 3%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDBoost && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDBoost_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDBOOST_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o -MF CMakeFiles/RDBoost.dir/Wrap.cpp.o.d -o CMakeFiles/RDBoost.dir/Wrap.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDBoost/Wrap.cpp [ 3%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/RDGeneral/testDict.cpp [ 3%] Building CXX object Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++14 -MD -MT Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o -MF CMakeFiles/testMatrices.dir/testMatrices.cpp.o.d -o CMakeFiles/testMatrices.dir/testMatrices.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/Numerics/testMatrices.cpp [ 3%] Linking CXX executable testConcurrentQueue cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-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/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -o testConcurrentQueue ../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 3%] Built target testConcurrentQueue make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/Code/Catalogs /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/Catalogs /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 3%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o -MF CMakeFiles/Catalogs.dir/Catalog.cpp.o.d -o CMakeFiles/Catalogs.dir/Catalog.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/Catalogs/Catalog.cpp [ 3%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o ../../../lib/libRDKitEigenSolvers.so.1.2022.03.2 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2022.03.2 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 3%] Built target EigenSolvers make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/Code/Query /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/Query /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/build make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 3%] Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/Query && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++14 -MD -MT Code/Query/CMakeFiles/testQuery.dir/test.cpp.o -MF CMakeFiles/testQuery.dir/test.cpp.o.d -o CMakeFiles/testQuery.dir/test.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/Query/test.cpp [ 3%] Building CXX object Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_main.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/catch2 -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++14 -MD -MT Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_main.cpp.o -MF CMakeFiles/logTestsCatch.dir/catch_main.cpp.o.d -o CMakeFiles/logTestsCatch.dir/catch_main.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDGeneral/catch_main.cpp [ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/DataStructs/ExplicitBitVect.cpp [ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o -MF CMakeFiles/DataStructs.dir/Utils.cpp.o.d -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/DataStructs/Utils.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/smart_ptr.hpp:19, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/Numerics/Vector.h:23, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDBoost/Wrap.h:17, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDBoost/Wrap.cpp:15: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 3%] Linking CXX executable testMatrices cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-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/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 3%] Built target testMatrices make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/Code/DataManip/MetricMatrixCalc /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 3%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++14 -MD -MT Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -MF CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o.d -o 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/SimDivPickers/DistPicker.cpp [ 3%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogParams.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/Catalogs/CatalogParams.cpp [ 3%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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&& /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDBoost.so.1.2022.03.2 ../../lib/libRDKitRDBoost.so.1 ../../lib/libRDKitRDBoost.so [ 4%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/SimDivPickers/HierarchicalClusterPicker.cpp [ 4%] Built target testMatCalc make -f 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-c /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDBoost/Wrap/RDBase.cpp [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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-ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/DataStructs/DiscreteDistMat.cpp [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/DataStructs/DiscreteValueVect.cpp [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/DataStructs/FPBReader.cpp [ 5%] Linking CXX executable testRDValue cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDValue.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDValue.dir/testRDValue.cpp.o -o testRDValue ../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 5%] Built target testRDValue make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/Code/ML/Cluster/Murtagh /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 5%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DClustering_EXPORTS -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o -MF CMakeFiles/Clustering.dir/Clustering.cpp.o.d -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/ML/Cluster/Murtagh/Clustering.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDBoost/python.h:3, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDBoost/Wrap/RDBase.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 5%] Linking CXX executable testQuery cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 5%] Built target testQuery [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/DataStructs/MultiFPBReader.cpp [ 5%] Linking CXX executable testDict cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDict.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDict.dir/testDict.cpp.o -o testDict ../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl [ 5%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2022.03.2 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2022.03.2 ../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2022.03.2 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so [ 5%] Built target testDict make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 5%] Built target SimDivPickers make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/Code/SimDivPickers /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/SimDivPickers /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' 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++14 -MD -MT Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -MF CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o.d -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/SimDivPickers/testPickers.cpp [ 5%] Linking CXX executable testSimDivPickers cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers ../../lib/libRDKitSimDivPickers.so.1.2022.03.2 ../../lib/libRDKithc.so.1.2022.03.2 ../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 5%] Built target testSimDivPickers In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/smart_ptr.hpp:19, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/Numerics/Vector.h:23, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDBoost/Wrap.h:17, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/ML/Cluster/Murtagh/Clustering.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 5%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o ../../../../lib/libRDKithc.so.1.2022.03.2 ../../../../lib/libRDKitRDBoost.so.1.2022.03.2 ../../../../lib/libRDKitRDGeneral.so.1.2022.03.2 -ldl /usr/lib/x86_64-linux-gnu/libpython3.10.so /usr/lib/x86_64-linux-gnu/libboost_python310.so -lpthread make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 5%] Built target Clustering [ 5%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2022.03.2 CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/DataStructs.dir/FPBReader.cpp.o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o ../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2022.03.2 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 5%] Built target DataStructs make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/Code/Geometry /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/Geometry /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/Code/DataStructs 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/Geometry/Transform2D.cpp [ 5%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 5%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -MF CMakeFiles/cDataStructs.dir/DataStructs.cpp.o.d -o CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/DataStructs/Wrap/DataStructs.cpp [ 5%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++14 -MD -MT Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -MF CMakeFiles/testFPB.dir/testFPB.cpp.o.d 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-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -MF CMakeFiles/RDGeometryLib.dir/point.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/Geometry/point.cpp make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build [ 5%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMetricMatrixCalc_EXPORTS -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -MF CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o.d -o CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 5%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++14 -MD -MT Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -MF 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'/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 5%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/DataStructs/testDatastructs.cpp [ 5%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o [ 5%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/Geometry/Transform3D.cpp cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/Geometry/UniformGrid3D.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDBoost/python.h:3, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDBoost/python.h:3, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/DataStructs/Wrap/DataStructs.cpp:13: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 5%] Linking CXX executable testFPB cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB ../../lib/libRDKitDataStructs.so.1.2022.03.2 ../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 5%] Built target testFPB [ 5%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o ../../../../lib/libRDKitDataStructs.so.1.2022.03.2 ../../../../lib/libRDKitRDBoost.so.1.2022.03.2 /usr/lib/x86_64-linux-gnu/libpython3.10.so /usr/lib/x86_64-linux-gnu/libboost_python310.so ../../../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl [ 5%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -MF CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/Geometry/GridUtils.cpp make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 5%] Built target rdMetricMatrixCalc make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/Code/SimDivPickers /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/SimDivPickers /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/catch2 -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++14 -MD -MT Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/SimDivPickers/catch_tests.cpp [ 5%] Linking CXX executable testMultiFPB cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB ../../lib/libRDKitDataStructs.so.1.2022.03.2 ../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 5%] Built target testMultiFPB make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/Code/SimDivPickers/Wrap /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 5%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/SimDivPickers/Wrap/MaxMinPicker.cpp make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/Code/ML/InfoTheory /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/ML/InfoTheory /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 5%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/ML/InfoTheory/InfoBitRanker.cpp [ 5%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/DataStructs/Wrap/DiscreteValueVect.cpp [ 6%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -MF CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/DataStructs/Wrap/SparseIntVect.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDBoost/python.h:3, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/SimDivPickers/Wrap/MaxMinPicker.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 6%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2022.03.2 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2022.03.2 ../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDBoost/python.h:3, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/DataStructs/Wrap/SparseIntVect.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2022.03.2 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 6%] Built target RDGeometryLib [ 6%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/SimDivPickers/Wrap/LeaderPicker.cpp [ 6%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-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/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitInfoTheory.so.1 -o ../../../lib/libRDKitInfoTheory.so.1.2022.03.2 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o ../../../lib/libRDKitDataStructs.so.1.2022.03.2 ../../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2022.03.2 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 6%] Built target InfoTheory make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-8H2dlr/rdkit-202203.2 /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDBoost/python.h:3, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/DataStructs/Wrap/DiscreteValueVect.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build make[4]: Entering directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 6%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o -MF CMakeFiles/GraphMol.dir/Atom.cpp.o.d -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/Atom.cpp [ 6%] Linking CXX executable testDataStructs cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../lib/libRDKitDataStructs.so.1.2022.03.2 ../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 6%] Built target testDataStructs [ 6%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -MF CMakeFiles/GraphMol.dir/QueryAtom.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/QueryAtom.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDBoost/python.h:3, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/SimDivPickers/Wrap/LeaderPicker.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 6%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -MF CMakeFiles/GraphMol.dir/QueryBond.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/QueryBond.cpp [ 6%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp c++: fatal error: Killed signal terminated program cc1plus compilation terminated. make[4]: *** [Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make:79: Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o] Error 1 make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:3652: Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/all] Error 2 make[3]: *** Waiting for unfinished jobs.... [ 6%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/DataStructs/Wrap/wrap_SparseBV.cpp c++: fatal error: Killed signal terminated program cc1plus compilation terminated. make[4]: *** [Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make:107: Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o] Error 1 make[4]: *** Waiting for unfinished jobs.... [ 6%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp c++: fatal error: Killed signal terminated program cc1plus compilation terminated. make[4]: *** [Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make:93: Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_main.cpp.o] Error 1 make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:3599: Code/RDGeneral/CMakeFiles/logTestsCatch.dir/all] Error 2 [ 7%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/Bond.cpp [ 7%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/MolOps.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDBoost/python.h:3, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp:13: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 7%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -MF CMakeFiles/GraphMol.dir/FindRings.cpp.o.d -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/FindRings.cpp [ 7%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/ROMol.cpp c++: fatal error: Killed signal terminated program cc1plus compilation terminated. make[4]: *** [Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make:79: Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o] Error 1 make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:12051: Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/all] Error 2 [ 7%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/RWMol.cpp [ 7%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/PeriodicTable.cpp [ 7%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/atomic_data.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/smart_ptr.hpp:19, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/Numerics/Vector.h:23, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDBoost/Wrap.h:17, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/DataStructs/Wrap/wrap_SparseBV.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/smart_ptr.hpp:19, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/Numerics/Vector.h:23, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/RDBoost/Wrap.h:17, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 7%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/FindRings.cpp: In function ‘void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)’: /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/FindRings.cpp:1348:36: warning: unused parameter ‘mol’ [-Wunused-parameter] 1348 | void findRingFamilies(const ROMol &mol) { | ~~~~~~~~~~~~~^~~ /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/SimDivFilters/rdSimDivPickers.so CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o ../../../lib/libRDKitSimDivPickers.so.1.2022.03.2 ../../../lib/libRDKitDataStructs.so.1.2022.03.2 ../../../lib/libRDKitRDBoost.so.1.2022.03.2 ../../../lib/libRDKithc.so.1.2022.03.2 /usr/lib/x86_64-linux-gnu/libpython3.10.so /usr/lib/x86_64-linux-gnu/libboost_python310.so ../../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 7%] Built target rdSimDivPickers [ 7%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/QueryOps.cpp [ 7%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/MolPickler.cpp [ 8%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/Canon.cpp [ 8%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/AtomIterators.cpp [ 8%] Linking CXX executable dictTestsCatch cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/dictTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o CMakeFiles/dictTestsCatch.dir/catch_main.cpp.o -o dictTestsCatch ../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 8%] Built target dictTestsCatch [ 8%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o -MF CMakeFiles/GraphMol.dir/BondIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/BondIterators.cpp make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:3813: Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all] Error 2 [ 8%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/Aromaticity.cpp /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/MolPickler.cpp: In instantiation of ‘static RDKit::Atom* RDKit::MolPickler::_addAtomFromPickle(std::istream&, RDKit::ROMol*, RDGeom::Point3D&, int, bool) [with T = int; std::istream = std::basic_istream]’: /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/MolPickler.cpp:1081:39: required from ‘static void RDKit::MolPickler::_depickle(std::istream&, RDKit::ROMol*, int, int, unsigned int) [with T = int; std::istream = std::basic_istream]’ /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/MolPickler.cpp:854:27: required from here /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/MolPickler.cpp:1666:37: warning: comparison is always false due to limited range of data type [-Wtype-limits] 1666 | if ((tmpChar < 0 || tmpChar > 127) && version > 9000) { | ~~~~~~~~^~~~~ /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/MolPickler.cpp: In instantiation of ‘static RDKit::Atom* RDKit::MolPickler::_addAtomFromPickle(std::istream&, RDKit::ROMol*, RDGeom::Point3D&, int, bool) [with T = unsigned char; std::istream = std::basic_istream]’: /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/MolPickler.cpp:1081:39: required from ‘static void RDKit::MolPickler::_depickle(std::istream&, RDKit::ROMol*, int, int, unsigned int) [with T = unsigned char; std::istream = std::basic_istream]’ /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/MolPickler.cpp:856:33: required from here /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/MolPickler.cpp:1666:37: warning: comparison is always false due to limited range of data type [-Wtype-limits] [ 8%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -MF CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o.d -o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/ConjugHybrid.cpp [ 8%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/AddHs.cpp [ 8%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/Matrices.cpp [ 9%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/Chirality.cpp [ 9%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/RingInfo.cpp [ 9%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o -MF CMakeFiles/GraphMol.dir/Conformer.cpp.o.d -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/Conformer.cpp [ 9%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/Renumber.cpp [ 9%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -MF CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o.d -o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/AdjustQuery.cpp [ 9%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/Resonance.cpp [ 9%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/StereoGroup.cpp [ 9%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o -MF CMakeFiles/GraphMol.dir/new_canon.cpp.o.d -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/new_canon.cpp [ 9%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/SubstanceGroup.cpp [ 10%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/FindStereo.cpp [ 10%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-8H2dlr/rdkit-202203.2/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-8H2dlr/rdkit-202203.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++14 -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/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/MonomerInfo.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/property_map/vector_property_map.hpp:14, from /usr/include/boost/property_map/property_map.hpp:602, from /usr/include/boost/graph/adjacency_list.hpp:27, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/ROMol.h:27, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/GraphMol.h:19, from /build/rdkit-8H2dlr/rdkit-202203.2/Code/GraphMol/AdjustQuery.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 10%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-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/rdkit-8H2dlr/rdkit-202203.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2022.03.2 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 ../../lib/libRDKitRDGeometryLib.so.1.2022.03.2 ../../lib/libRDKitDataStructs.so.1.2022.03.2 ../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl cd /build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitGraphMol.so.1.2022.03.2 ../../lib/libRDKitGraphMol.so.1 ../../lib/libRDKitGraphMol.so make[4]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' [ 10%] Built target GraphMol make[3]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' make[2]: *** [Makefile:169: all] Error 2 make[2]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2/obj-x86_64-linux-gnu' dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j10 VERBOSE=1 returned exit code 2 make[1]: *** [debian/rules:92: override_dh_auto_build] Error 25 make[1]: Leaving directory '/build/rdkit-8H2dlr/rdkit-202203.2' make: *** [debian/rules:40: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 E: run_chroot failed: E: command failed: chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/rdkit-8H2dlr/rdkit-202203.2 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1651049389" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" W: listening on child socket failed: I: removing tempdir /tmp/mmdebstrap.t0nfn1mFkO... E: mmdebstrap failed to run mmdebstrap failed