Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/r/rdkit/rdkit_202009.4-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/rdkit-202009.4-1y0w2m122/rdkit_202009.4-1_amd64.buildinfo Get source package info: rdkit=202009.4-1 Source URL: http://snapshot.notset.fr/mr/package/rdkit/202009.4-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.49 bash=5.1-2 binutils=2.35.1-7 binutils-common=2.35.1-7 binutils-x86-64-linux-gnu=2.35.1-7 bison=2:3.7.5+dfsg-1 bsdextrautils=2.36.1-7 bsdutils=1:2.36.1-7 build-essential=12.9 bzip2=1.0.8-4 ca-certificates=20210119 catch2=2.13.4-2+b1 clang-11=1:11.0.1-2 cmake=3.18.4-2 cmake-data=3.18.4-2 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20200708+dd9ef66-5 debconf=1.5.74 debhelper=13.3.3 debianutils=4.11.2 dh-autoreconf=20 dh-python=4.20201102 dh-strip-nondeterminism=1.11.0-1 diffutils=1:3.7-5 docutils-common=0.16+dfsg-3 doxygen=1.9.1-1 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.13+20210201-1 file=1:5.39-3 findutils=4.8.0-1 flex=2.6.4-8 fontconfig=2.13.1-4.2 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 fonts-lmodern=2.004.5-6.1 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-4 gettext-base=0.21-4 grep=3.6-1 groff-base=1.22.4-6 gzip=1.10-2 hicolor-icon-theme=0.17-2 hostname=3.23 icu-devtools=67.1-6 imagemagick=8:6.9.11.60+dfsg-1 imagemagick-6-common=8:6.9.11.60+dfsg-1 imagemagick-6.q16=8:6.9.11.60+dfsg-1 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 latexmk=1:4.70b-0.2 lib32gcc-s1=10.2.1-6 lib32stdc++6=10.2.1-6 libacl1=2.2.53-10 libaom0=1.0.0.errata1-3 libapache-pom-java=18-1 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbinutils=2.35.1-7 libblas3=3.9.0-3 libblkid1=2.36.1-7 libboost-atomic1.74-dev=1.74.0-8 libboost-atomic1.74.0=1.74.0-8 libboost-chrono1.74-dev=1.74.0-8 libboost-chrono1.74.0=1.74.0-8 libboost-date-time1.74-dev=1.74.0-8 libboost-date-time1.74.0=1.74.0-8 libboost-dev=1.74.0.3 libboost-iostreams-dev=1.74.0.3 libboost-iostreams1.74-dev=1.74.0-8 libboost-iostreams1.74.0=1.74.0-8 libboost-python-dev=1.74.0.3 libboost-python1.74-dev=1.74.0-8 libboost-python1.74.0=1.74.0-8 libboost-regex-dev=1.74.0.3 libboost-regex1.74-dev=1.74.0-8 libboost-regex1.74.0=1.74.0-8 libboost-serialization1.74-dev=1.74.0-8 libboost-serialization1.74.0=1.74.0-8 libboost-system-dev=1.74.0.3 libboost-system1.74-dev=1.74.0-8 libboost-system1.74.0=1.74.0-8 libboost-thread-dev=1.74.0.3 libboost-thread1.74-dev=1.74.0-8 libboost-thread1.74.0=1.74.0-8 libboost1.74-dev=1.74.0-8 libbrotli-dev=1.0.9-2+b2 libbrotli1=1.0.9-2+b2 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-4 libc-bin=2.31-9 libc-dev-bin=2.31-9 libc6=2.31-9 libc6-dev=2.31-9 libc6-i386=2.31-9 libcairo-gobject2=1.16.0-5 libcairo2=1.16.0-5 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libclang-common-11-dev=1:11.0.1-2 libclang-cpp11=1:11.0.1-2 libclang1-11=1:11.0.1-2 libcmark-gfm-extensions0=0.29.0.gfm.0-6 libcmark-gfm0=0.29.0.gfm.0-6 libcom-err2=1.46.1-1 libcommons-logging-java=1.2-2 libcommons-parent-java=43-1 libcoordgen-dev=1.4.2-1 libcoordgen1=1.4.2-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-7 libctf0=2.35.1-7 libcurl4=7.74.0-1.1 libdatrie1=0.2.13-1 libdav1d4=0.7.1-3 libdb5.3=5.3.28+dfsg1-0.8 libde265-0=1.0.8-1 libdebconfclient0=0.256 libdebhelper-perl=13.3.3 libdeflate0=1.7-1 libdpkg-perl=1.20.7.1 libedit2=3.1-20191231-2+b1 libeigen3-dev=3.3.9-2 libelf1=0.183-1 libexpat1=2.2.10-1 libexpat1-dev=2.2.10-1 libffi-dev=3.3-6 libffi7=3.3-6 libfftw3-double3=3.3.8-2 libfile-stripnondeterminism-perl=1.11.0-1 libfontbox-java=1:1.8.16-2 libfontconfig1=2.13.1-4.2 libfreetype-dev=2.10.4+dfsg-1 libfreetype6=2.10.4+dfsg-1 libfreetype6-dev=2.10.4+dfsg-1 libfribidi0=1.0.8-2 libgc1=1:8.0.4-3 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-3 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgdk-pixbuf-2.0-0=2.42.2+dfsg-1 libgdk-pixbuf2.0-common=2.42.2+dfsg-1 libgfortran5=10.2.1-6 libglib2.0-0=2.66.7-1 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.0-7 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.18.3-4 libharfbuzz0b=2.7.4-1 libheif1=1.11.0-1 libhogweed6=3.7-2 libice6=2:1.0.10-1 libicu-dev=67.1-6 libicu67=67.1-6 libidn2-0=2.3.0-5 libimagequant0=2.12.2-1.1 libisl23=0.23-1 libitm1=10.2.1-6 libjbig0=2.1-3.1+b2 libjpeg62-turbo=1:2.0.6-1 libjs-jquery=3.5.1+dfsg+~3.5.5-7 libjs-sphinxdoc=3.4.3-1 libjs-underscore=1.9.1~dfsg-1 libjsoncpp24=1.9.4-4 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkpathsea6=2020.20200327.54578-6 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblapack3=3.9.0-3 liblcms2-2=2.12~rc1-2 libldap-2.4-2=2.4.57+dfsg-2 libllvm11=1:11.0.1-2 liblqr-1-0=0.4.2-2.1 liblsan0=10.2.1-6 libltdl7=2.4.6-15 liblz4-1=1.9.3-1 liblzma5=5.2.5-1.0 libmaeparser-dev=1.2.4-1+b1 libmaeparser1=1.2.4-1+b1 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmagickcore-6.q16-6=8:6.9.11.60+dfsg-1 libmagickwand-6.q16-6=8:6.9.11.60+dfsg-1 libmd0=1.0.3-3 libmount1=2.36.1-7 libmpc3=1.2.0-1 libmpdec3=2.5.1-1 libmpfr6=4.1.0-3 libncurses-dev=6.2+20201114-2 libncurses6=6.2+20201114-2 libncursesw6=6.2+20201114-2 libnettle8=3.7-2 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnuma1=2.0.12-1+b1 libobjc-10-dev=10.2.1-6 libobjc4=10.2.1-6 libopenjp2-7=2.4.0-3 libp11-kit0=0.23.22-1 libpam-modules=1.4.0-4 libpam-modules-bin=1.4.0-4 libpam-runtime=1.4.0-4 libpam0g=1.4.0-4 libpango-1.0-0=1.46.2-3 libpangocairo-1.0-0=1.46.2-3 libpangoft2-1.0-0=1.46.2-3 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libpdfbox-java=1:1.8.16-2 libperl5.32=5.32.1-2 libpfm4=4.11.1+git8-gc96ebc0-1 libpipeline1=1.5.3-1 libpixman-1-0=0.40.0-1 libpng-dev=1.6.37-3 libpng16-16=1.6.37-3 libpq-dev=13.2-1 libpq5=13.2-1 libprocps8=2:3.3.17-4 libpsl5=0.21.0-1.2 libptexenc1=2020.20200327.54578-6 libpython3-dev=3.9.1-1 libpython3-stdlib=3.9.1-1 libpython3.9=3.9.1-4 libpython3.9-dev=3.9.1-4 libpython3.9-minimal=3.9.1-4 libpython3.9-stdlib=3.9.1-4 libquadmath0=10.2.1-6 libreadline8=8.1-1 librhash0=1.4.1-1 librsvg2-2=2.50.3+dfsg-1 librsvg2-bin=2.50.3+dfsg-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2.1 libsasl2-modules-db=2.1.27+dfsg-2.1 libseccomp2=2.5.1-1 libselinux1=3.1-3 libsemanage-common=3.1-1 libsemanage1=3.1-1+b2 libsepol1=3.1-1 libsigsegv2=2.13-1 libsm6=2:1.2.3-1 libsmartcols1=2.36.1-7 libsqlite3-0=3.34.1-2 libsqlite3-dev=3.34.1-2 libssh2-1=1.9.0-2 libssl1.1=1.1.1j-1 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsynctex2=2020.20200327.54578-6 libsystemd0=247.3-1 libtasn1-6=4.16.0-2 libteckit0=2.5.10+ds1-3 libtexlua53=2020.20200327.54578-6 libtexluajit2=2020.20200327.54578-6 libthai-data=0.1.28-3 libthai0=0.1.28-3 libtiff5=4.2.0-1 libtinfo-dev=6.2+20201114-2 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.3-1 libunistring2=0.9.10-4 libuuid1=2.36.1-7 libuv1=1.40.0-1 libwebp6=0.6.1-2+b1 libwebpdemux2=0.6.1-2+b1 libwebpmux3=0.6.1-2+b1 libx11-6=2:1.7.0-2 libx11-data=2:1.7.0-2 libx265-192=3.4-2 libxapian30=1.4.18-2 libxau6=1:1.0.9-1 libxaw7=2:1.0.13-1.1 libxcb-render0=1.14-3 libxcb-shm0=1.14-3 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1.1 libxi6=2:1.7.10-1 libxml2=2.9.10+dfsg-6.3+b1 libxmu6=2:1.1.2-2+b3 libxpm4=1:3.5.12-1 libxrender1=1:0.9.10-1 libxt6=1:1.2.0-1 libyaml-0-2=0.2.2-1 libz3-4=4.8.10-1 libz3-dev=4.8.10-1 libzstd1=1.4.8+dfsg-1 libzzip-0-13=0.13.62-3.2 linux-libc-dev=5.10.13-1 llvm-11=1:11.0.1-2 llvm-11-dev=1:11.0.1-2 llvm-11-runtime=1:11.0.1-2 llvm-11-tools=1:11.0.1-2 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 mailcap=3.68 make=4.3-4 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 mime-support=3.66 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 netbase=6.2 openssl=1.1.1j-1 pandoc=2.9.2.1-1+b1 pandoc-data=2.9.2.1-1 passwd=1:4.8.1-1 patch=2.7.6-7 perl=5.32.1-2 perl-base=5.32.1-2 perl-modules-5.32=5.32.1-2 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 postgresql-client-13=13.2-1 postgresql-client-common=225 postgresql-common=225 postgresql-server-dev-13=13.2-1 postgresql-server-dev-all=225 preview-latex-style=12.2-1 procps=2:3.3.17-4 python-babel-localedata=2.8.0+dfsg.1-6 python3=3.9.1-1 python3-alabaster=0.7.8-1.1 python3-babel=2.8.0+dfsg.1-6 python3-certifi=2020.6.20-1 python3-chardet=4.0.0-1 python3-commonmark=0.9.1-3 python3-dateutil=2.8.1-5 python3-dev=3.9.1-1 python3-distutils=3.9.2-1 python3-docutils=0.16+dfsg-3 python3-idna=2.10-1 python3-imagesize=1.2.0-2 python3-jinja2=2.11.2-1 python3-lib2to3=3.9.2-1 python3-markupsafe=1.1.1-1+b3 python3-minimal=3.9.1-1 python3-numpy=1:1.19.5-1 python3-packaging=20.9-2 python3-pandas=1.1.5+dfsg-2 python3-pandas-lib=1.1.5+dfsg-2 python3-pil=8.1.0-1 python3-pkg-resources=52.0.0-1 python3-pygments=2.7.1+dfsg-1 python3-pyparsing=2.4.7-1 python3-recommonmark=0.6.0+ds-1 python3-requests=2.25.1+dfsg-2 python3-roman=2.0.0-5 python3-six=1.15.0-2 python3-snowballstemmer=2.1.0-1 python3-sphinx=3.4.3-1 python3-sqlalchemy=1.3.22+ds1-1 python3-tz=2021.1-1 python3-urllib3=1.26.2-1 python3-yaml=5.3.1-3+b1 python3.9=3.9.1-4 python3.9-dev=3.9.1-4 python3.9-minimal=3.9.1-4 rapidjson-dev=1.1.0+dfsg2-7 readline-common=8.1-1 sed=4.7-1 sensible-utils=0.0.14 sgml-base=1.30 shared-mime-info=2.0-1 sphinx-common=3.4.3-1 ssl-cert=1.1.0 sysvinit-utils=2.96-5 t1utils=1.41-4 tar=1.34+dfsg-1 tex-common=6.16 texlive-base=2020.20210202-3 texlive-binaries=2020.20200327.54578-6 texlive-fonts-recommended=2020.20210202-3 texlive-latex-base=2020.20210202-3 texlive-latex-extra=2020.20210202-1 texlive-latex-recommended=2020.20210202-3 texlive-pictures=2020.20210202-3 tzdata=2021a-1 ucf=3.0043 util-linux=2.36.1-7 x11-common=1:7.7+22 xdg-utils=1.1.3-4 xml-core=0.18+nmu1 xz-utils=5.2.5-1.0 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210902T205533Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210218T111050Z/ 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=202009.4-1 && mkdir -p /build/rdkit-TKP8Bz && dpkg-source --no-check -x /*.dsc /build/rdkit-TKP8Bz/rdkit-202009.4 && chown -R builduser:builduser /build/rdkit-TKP8Bz" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/rdkit-TKP8Bz/rdkit-202009.4 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1613904125" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/rdkit-TKP8Bz /tmp/rdkit-202009.4-1y0w2m122 bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210218T111050Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.uspI2qVYGf 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.uspI2qVYGf Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-7). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210218T111050Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210218T111050Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1118 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 ... 4662 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-9) ... 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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210902T205533Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210218T111050Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.uspI2qVYGf Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210902T205533Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20210218T111050Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20210902T205533Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210902T205533Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210902T205533Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20210902T205533Z unstable/main amd64 Packages [11.9 MB] Fetched 34.6 MB in 30s (1158 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.uspI2qVYGf I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d rdkit=202009.4-1 && mkdir -p /build/rdkit-TKP8Bz && dpkg-source --no-check -x /*.dsc /build/rdkit-TKP8Bz/rdkit-202009.4 && chown -R builduser:builduser /build/rdkit-TKP8Bz"' exec /tmp/mmdebstrap.uspI2qVYGf 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 51.8 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main rdkit 202009.4-1 (dsc) [2821 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main rdkit 202009.4-1 (tar) [51.7 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main rdkit 202009.4-1 (diff) [101 kB] Fetched 51.8 MB in 41s (1266 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'rdkit_202009.4-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting rdkit in /build/rdkit-TKP8Bz/rdkit-202009.4 dpkg-source: info: unpacking rdkit_202009.4.orig.tar.xz dpkg-source: info: unpacking rdkit_202009.4-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying NoDownloads.patch dpkg-source: info: applying postgres_Makefile_fixes.patch dpkg-source: info: applying postgres_disable_failing_tests.patch dpkg-source: info: applying sphinx_imgconverter.patch dpkg-source: info: applying catch2_header.patch dpkg-source: info: applying postgres_alternative_test_outputs.patch dpkg-source: info: applying postgres_compile_fixes.patch dpkg-source: info: applying sphinx_compile_fixes.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/rdkit-TKP8Bz/rdkit-202009.4 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1613904125" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.uspI2qVYGf dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202009.4-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael Banck dpkg-source --before-build . dpkg-buildpackage: info: host architecture 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-TKP8Bz/rdkit-202009.4' find /build/rdkit-TKP8Bz/rdkit-202009.4 -name "*.pyc" | xargs rm -f rm -f -r Projects/DbCLI/testData/bzr/ rdkit/Chem/inchi.py rm -f -r Docs/Book/_build Code/docs rdkit/docs Code/doxygen_sqlite3.db rm -f \ Code/ForceField/MMFF/test_data/MMFF94_dative_min.sdf \ Code/ForceField/MMFF/test_data/MMFF94_dative_min_from_SMILES.sdf \ Code/ForceField/MMFF/test_data/MMFF94_hypervalent_min.sdf \ Code/ForceField/MMFF/test_data/MMFF94_hypervalent_min_from_SMILES.sdf \ Code/ForceField/MMFF/test_data/MMFF94_reference.log \ Code/ForceField/MMFF/test_data/MMFF94s_reference.log \ Code/ForceField/MMFF/test_data/testMMFFForceField.log \ Code/GraphMol/Depictor/test_data/cis_trans_cpp.out.sdf \ Code/GraphMol/Depictor/test_data/collisions.out.sdf \ Code/GraphMol/Depictor/test_data/first_200.out.sdf \ Code/GraphMol/Depictor/test_data/test1.out.sdf \ Code/GraphMol/FileParsers/test_data/blah.sdf \ Code/GraphMol/FileParsers/test_data/cdk2_stereo.sdf \ Code/GraphMol/FileParsers/test_data/outNCI_few.sdf \ Code/GraphMol/FileParsers/test_data/outNCI_few.tdt \ Code/GraphMol/FileParsers/test_data/outNCI_first_200.props.sdf \ Code/GraphMol/FileParsers/test_data/outSmiles.csv \ Code/GraphMol/ForceFieldHelpers/UFF/test_data/Issue62.sdf \ Code/GraphMol/MolAlign/test_data/ref_e2_pyCrippenO3A.sdf \ Code/GraphMol/SLNParse/lex.yysln.cpp \ Code/GraphMol/SLNParse/sln.tab.cpp \ Code/GraphMol/SLNParse/sln.tab.hpp \ Code/GraphMol/SmilesParse/lex.yysmarts.cpp \ Code/GraphMol/SmilesParse/lex.yysmiles.cpp \ Code/GraphMol/SmilesParse/smarts.tab.cpp \ Code/GraphMol/SmilesParse/smarts.tab.hpp \ Code/GraphMol/SmilesParse/smiles.tab.cpp \ Code/GraphMol/SmilesParse/smiles.tab.hpp \ Code/GraphMol/Wrap/test_data/outNCI_few.sdf \ Code/GraphMol/Wrap/test_data/outSmiles.txt \ Code/RDGeneral/versions.cpp \ Docs/Book/Cartridge.rst \ Docs/Book/Cookbook.rst \ Docs/Book/Install.rst \ Docs/Book/Overview.rst \ rdkit/ML/Data/test_data/testgeneral.dat.pkl \ rdkit/ML/Data/test_data/testquant.qdat.pkl rm -f Code/RDGeneral/versions.h rdkit/sping/tests/testallps.ps dh_auto_clean dh_auto_clean: warning: Compatibility levels before 10 are deprecated (level 9 in use) pg_buildext clean /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit build-%v rm -rf build-*/ make[1]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4' dh_clean -O--buildsystem=cmake -O--parallel dh_clean: warning: Compatibility levels before 10 are deprecated (level 9 in use) debian/rules build-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-TKP8Bz/rdkit-202009.4' dh_auto_configure -- -DCMAKE_BUILD_TYPE=None -DCMAKE_SKIP_RPATH=ON -DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_THREADSAFE_SSS=ON -DRDK_BUILD_PYTHON_WRAPPERS=ON -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_USE_URF=OFF -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=/usr -DCATCH_DIR=/usr/include/catch2 -DPYTHON_EXECUTABLE=/usr/bin/python3.9 ../ dh_auto_configure: warning: Compatibility levels before 10 are deprecated (level 9 in use) cd obj-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_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 -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=/usr -DCATCH_DIR=/usr/include/catch2 -DPYTHON_EXECUTABLE=/usr/bin/python3.9 ../ .. -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Found Catch2: /usr/include/catch2 CATCH: /usr/include/catch2 -- Found PythonInterp: /usr/bin/python3.9 (found version "3.9.1") -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.9.so (found version "3.9.1+") CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:279 (find_package) CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:279 (find_package) CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:2018 (message): No header defined for python-py39; skipping header check (note: header-only libraries have no designated component) Call Stack (most recent call first): CMakeLists.txt:279 (find_package) CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:279 (find_package) CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:279 (find_package) Python Install directory /usr/lib/python3/dist-packages PYTHON Py_ENABLE_SHARED: 1 PYTHON USING LINK LINE: -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:387 (find_package) -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.58.0") found components: serialization == Using strict rotor definition CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) External/CoordGen/CMakeLists.txt:9 (find_package) CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) External/CoordGen/CMakeLists.txt:9 (find_package) CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) External/CoordGen/CMakeLists.txt:9 (find_package) -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.58.0") found components: system iostreams regex -- maeparser include dir set as '/usr/include' -- maeparser libraries set as '/usr/lib/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 CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) Code/RDStreams/CMakeLists.txt:4 (find_package) CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) Code/RDStreams/CMakeLists.txt:4 (find_package) -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.58.0") found components: iostreams regex CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) Code/GraphMol/FileParsers/CMakeLists.txt:21 (find_package) CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) Code/GraphMol/FileParsers/CMakeLists.txt:21 (find_package) CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) Code/GraphMol/FileParsers/CMakeLists.txt:21 (find_package) -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.58.0") found components: system iostreams regex -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") == Updating Filters.cpp from pains file == Done updating pains files -- Found Freetype: /usr/lib/x86_64-linux-gnu/libfreetype.so (found version "2.10.4") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4' debian/rules override_dh_auto_build make[1]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4' dh_auto_build dh_auto_build: warning: Compatibility levels before 10 are deprecated (level 9 in use) cd obj-x86_64-linux-gnu && make -j4 VERBOSE=1 make[2]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/rdkit-TKP8Bz/rdkit-202009.4 -B/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/CMakeFiles /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/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 -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/depend make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/External/CoordGen /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/External/INCHI-API /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/INCHI-API /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/External/catch /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/catch /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/catch/CMakeFiles/catch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd 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Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/INCHI-API/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/INCHI-API/CMakeFiles/inchi_support.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/depend.internal". 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Scanning dependencies of target hc Scanning dependencies of target RDStreams make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' Scanning dependencies of target RDGeneral make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 0%] Building CXX object Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDStreams && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RDSTREAMS_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDStreams_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDStreams.dir/streams.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDStreams/streams.cpp [ 0%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o [ 0%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -o CMakeFiles/hc.dir/hc.c.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/Cluster/Murtagh/hc.c cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -o CMakeFiles/hc.dir/hcdriver.c.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/Cluster/Murtagh/hcdriver.c [ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/Invariant.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/Invariant.cpp [ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/types.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/types.cpp [ 0%] Linking C shared library ../../../../lib/libRDKithc.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKithc.so.1 -o ../../../../lib/libRDKithc.so.1.2020.09.4 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o -lpthread cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2020.09.4 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 0%] Built target hc [ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/utils.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/utils.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/RDLog.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/RDLog.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/LocaleSwitcher.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/versions.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/versions.cpp [ 1%] Linking CXX shared library ../../lib/libRDKitRDStreams.so cd 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[ 1%] Built target RDStreams [ 1%] Linking CXX shared library ../../lib/libRDKitRDGeneral.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeneral.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o ../../lib/libRDKitRDGeneral.so.1.2020.09.4 CMakeFiles/RDGeneral.dir/Invariant.cpp.o CMakeFiles/RDGeneral.dir/types.cpp.o CMakeFiles/RDGeneral.dir/utils.cpp.o CMakeFiles/RDGeneral.dir/RDLog.cpp.o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o CMakeFiles/RDGeneral.dir/versions.cpp.o -ldl -lpthread cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeneral.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1 ../../lib/libRDKitRDGeneral.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 1%] Built target RDGeneral make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/EigenSolvers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend.internal". Scanning dependencies of target testConcurrentQueue Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/depend.internal". make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build Scanning dependencies of target EigenSolvers make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build Scanning dependencies of target RDBoost make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' Scanning dependencies of target DataStructs make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/testConcurrentQueue.cpp [ 1%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDBoost.dir/Wrap.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.cpp [ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/BitVect.cpp [ 1%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DEigenSolvers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_EIGENSOLVERS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp [ 2%] Linking CXX executable testConcurrentQueue cd /build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 2%] Built target testConcurrentQueue make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake --color= [ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/SparseBitVect.cpp Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/depend.internal". Scanning dependencies of target testRDValue make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testRDValue.dir/testRDValue.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/testRDValue.cpp [ 2%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 2%] Built target EigenSolvers make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/depend.internal". Scanning dependencies of target testDict make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testDict.dir/testDict.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/testDict.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.cpp:15: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 2%] Linking CXX shared library ../../lib/libRDKitRDBoost.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDBoost.so.1 -o ../../lib/libRDKitRDBoost.so.1.2020.09.4 CMakeFiles/RDBoost.dir/Wrap.cpp.o ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../lib/libRDKitRDBoost.so.1 ../../lib/libRDKitRDBoost.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 2%] Built target RDBoost make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/depend.internal". Scanning dependencies of target testMatrices make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 2%] Building CXX object Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMatrices.dir/testMatrices.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/testMatrices.cpp [ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/ExplicitBitVect.cpp [ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/Utils.cpp [ 2%] Linking CXX executable testMatrices cd /build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 2%] Built target testMatrices make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Catalogs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Catalogs 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Scanning dependencies of target testQuery make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 3%] Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testQuery.dir/test.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/test.cpp [ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/BitOps.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/BitOps.cpp [ 3%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Catalogs/CatalogParams.cpp [ 3%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Catalogs/CatalogEntry.cpp [ 3%] Linking CXX shared library ../../lib/libRDKitCatalogs.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2020.09.4 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 3%] Built target Catalogs make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make 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Scanning dependencies of target testMatCalc make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 3%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp [ 3%] Linking CXX executable testDict cd /build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDict.dir/testDict.cpp.o -o testDict ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 3%] Built target testDict make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend.internal". 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-I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/Cluster/Murtagh/Clustering.cpp [ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/DiscreteDistMat.cpp [ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/FPBReader.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/FPBReader.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/Cluster/Murtagh/Clustering.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/HierarchicalClusterPicker.cpp [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/MultiFPBReader.cpp [ 5%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o ../../../../lib/libRDKithc.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so -lpthread make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 5%] Built target Clustering make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend.internal". Scanning dependencies of target rdBase make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 5%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/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 -DrdBase_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdBase.dir/RDBase.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap/RDBase.cpp [ 6%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2020.09.4 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2020.09.4 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 6%] Built target SimDivPickers make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend.internal". Scanning dependencies of target testSimDivPickers make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/testPickers.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap/RDBase.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 6%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2020.09.4 CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/DataStructs.dir/FPBReader.cpp.o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap/RDBase.cpp:14: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 6%] Built target DataStructs make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend.internal". Scanning dependencies of target testMultiFPB Scanning dependencies of target RDGeometryLib make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 6%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/testMultiFPB.cpp [ 6%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.cpp [ 6%] Linking CXX executable testSimDivPickers cd /build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers ../../lib/libRDKitSimDivPickers.so.1.2020.09.4 ../../lib/libRDKithc.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 6%] Built target testSimDivPickers make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/depend.internal". Scanning dependencies of target testFPB make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 6%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/testFPB.cpp [ 6%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Transform2D.cpp [ 6%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Transform3D.cpp [ 6%] Linking CXX executable testFPB cd /build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 6%] Built target testFPB make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/depend.internal". Scanning dependencies of target testDataStructs make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 6%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/testDatastructs.cpp [ 6%] Linking CXX executable testMultiFPB cd /build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 6%] Built target testMultiFPB make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend.internal". Scanning dependencies of target cDataStructs make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 7%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/Wrap/DataStructs.cpp [ 7%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/Wrap/DataStructs.cpp:13: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 8%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/GridUtils.cpp [ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/Wrap/DiscreteValueVect.cpp [ 8%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 8%] Built target RDGeometryLib make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend.internal". Scanning dependencies of target rdMetricMatrixCalc make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 8%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/Wrap/DiscreteValueVect.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 9%] Linking CXX executable testDataStructs cd /build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 9%] Built target testDataStructs [ 9%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/Wrap/wrap_SparseBV.cpp [ 9%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/Wrap/SparseIntVect.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 9%] Built target rdMetricMatrixCalc [ 9%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/Wrap/wrap_ExplicitBV.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/Wrap/wrap_SparseBV.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 9%] Linking CXX shared module ../../../rdkit/rdBase.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so -lpthread [ 9%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/Wrap/wrap_BitOps.cpp make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 9%] Built target rdBase make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend.internal". Scanning dependencies of target pickersTestsCatch make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 9%] Building CXX object Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/catch_tests.cpp [ 9%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/Wrap/wrap_FPB.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/Wrap/wrap_BitOps.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/Wrap/wrap_FPB.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 9%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/Wrap/wrap_Utils.cpp make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend.internal". Scanning dependencies of target rdSimDivPickers make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 9%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/Wrap/MaxMinPicker.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/Wrap/wrap_Utils.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 9%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/Wrap/LeaderPicker.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/Wrap/MaxMinPicker.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 10%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DataStructs/cDataStructs.so CMakeFiles/cDataStructs.dir/DataStructs.cpp.o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 10%] Built target cDataStructs make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/InfoTheory /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend.internal". Scanning dependencies of target InfoTheory make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 10%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/InfoTheory/InfoBitRanker.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/Wrap/LeaderPicker.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 10%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp [ 10%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitInfoTheory.so.1 -o ../../../lib/libRDKitInfoTheory.so.1.2020.09.4 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2020.09.4 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 10%] Built target InfoTheory make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ChemicalFeatures /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend.internal". Scanning dependencies of target ChemicalFeatures make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 10%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ChemicalFeatures/FreeChemicalFeature.cpp [ 11%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/Wrap/rdSimDivPickers.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp:13: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 11%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemicalFeatures.so.1 -o ../../lib/libRDKitChemicalFeatures.so.1.2020.09.4 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2020.09.4 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 11%] Built target ChemicalFeatures make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/depend.internal". Scanning dependencies of target GraphMol make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Atom.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/QueryAtom.cpp [ 11%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/SimDivFilters/rdSimDivPickers.so CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o ../../../lib/libRDKitSimDivPickers.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKithc.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 11%] Built target rdSimDivPickers [ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/QueryBond.cpp [ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Bond.cpp [ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolOps.cpp [ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FindRings.cpp [ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/ROMol.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ROMol.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FindRings.cpp: In function ‘void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FindRings.cpp:1367:36: warning: unused parameter ‘mol’ [-Wunused-parameter] 1367 | void findRingFamilies(const ROMol &mol) { | ~~~~~~~~~~~~~^~~ [ 11%] Linking CXX executable pickersTestsCatch cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickersTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -o pickersTestsCatch ../../lib/libRDKitSimDivPickers.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKithc.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RWMol.cpp make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 12%] Built target pickersTestsCatch make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Alignment /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu 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Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend.internal". Scanning dependencies of target Alignment make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 12%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ALIGNMENT_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Alignment/AlignPoints.cpp [ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/PeriodicTable.cpp [ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/atomic_data.cpp [ 12%] Linking CXX shared library ../../../lib/libRDKitAlignment.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2020.09.4 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 12%] Built target Alignment make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make 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Scanning dependencies of target testGrid make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 12%] Building CXX object Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/testGrid.cpp [ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/QueryOps.cpp [ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolPickler.cpp [ 12%] Linking CXX executable testGrid cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGrid.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGrid.dir/testGrid.cpp.o -o testGrid ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 12%] Built target testGrid [ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Canon.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Canon.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolPickler.cpp: In instantiation of ‘static RDKit::Atom* RDKit::MolPickler::_addAtomFromPickle(std::istream&, RDKit::ROMol*, RDGeom::Point3D&, int, bool) [with T = int; std::istream = std::basic_istream]’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolPickler.cpp:1139:39: required from ‘static void RDKit::MolPickler::_depickle(std::istream&, RDKit::ROMol*, int, int) [with T = int; std::istream = std::basic_istream]’ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolPickler.cpp:928:59: required from here /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolPickler.cpp:1684:37: warning: comparison is always false due to limited range of data type [-Wtype-limits] 1684 | if ((tmpChar < 0 || tmpChar > 127) && version > 9000) { | ~~~~~~~~^~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolPickler.cpp: In instantiation of ‘static RDKit::Atom* RDKit::MolPickler::_addAtomFromPickle(std::istream&, RDKit::ROMol*, RDGeom::Point3D&, int, bool) [with T = unsigned char; std::istream = std::basic_istream]’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolPickler.cpp:1139:39: required from ‘static void RDKit::MolPickler::_depickle(std::istream&, RDKit::ROMol*, int, int) [with T = unsigned char; std::istream = std::basic_istream]’ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolPickler.cpp:930:65: required from here /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolPickler.cpp:1684:37: warning: comparison is always false due to limited range of data type [-Wtype-limits] [ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/AtomIterators.cpp [ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/BondIterators.cpp [ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Aromaticity.cpp [ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Kekulize.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Kekulize.cpp [ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDiscriminators.cpp [ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ConjugHybrid.cpp [ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/AddHs.cpp make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/depend.internal". Scanning dependencies of target testTransforms make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 13%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/testTransforms.cpp [ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Matrices.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Matrices.cpp [ 13%] Linking CXX executable testTransforms cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testTransforms.dir/testTransforms.cpp.o -o testTransforms ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 13%] Built target testTransforms [ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Chirality.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Chirality.cpp [ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RingInfo.cpp make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend.internal". Scanning dependencies of target rdGeometry make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 13%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/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 -DrdGeometry_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Wrap/Point.cpp [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Conformer.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Wrap/Point.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Renumber.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Renumber.cpp [ 14%] Linking CXX executable geometryTestsCatch cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/geometryTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -o geometryTestsCatch ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 14%] Built target geometryTestsCatch [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/AdjustQuery.cpp [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Resonance.cpp [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/StereoGroup.cpp [ 14%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/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 -DrdGeometry_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Wrap/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/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-TKP8Bz/rdkit-202009.4/Code/GraphMol/ROMol.h:27, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/GraphMol.h:19, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/AdjustQuery.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/depend.internal". Scanning dependencies of target testConrec make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 14%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testConrec.dir/testConrec.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/testConrec.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Wrap/UniformGrid3D.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/new_canon.cpp [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstanceGroup.cpp [ 15%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/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 -DrdGeometry_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Wrap/rdGeometry.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Wrap/rdGeometry.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 15%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 15%] Built target rdGeometry make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Alignment /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend.internal". Scanning dependencies of target testAlignment make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 15%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testAlignment.dir/testAlignment.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Alignment/testAlignment.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/FindStereo.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FindStereo.cpp make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Alignment/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend.internal". Scanning dependencies of target rdAlignment make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 15%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/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 -DrdAlignment_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Alignment/Wrap/rdAlignment.cpp [ 15%] Linking CXX executable testAlignment cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAlignment.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAlignment.dir/testAlignment.cpp.o -o testAlignment ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 15%] Built target testAlignment make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/InfoTheory/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend.internal". Scanning dependencies of target rdInfoTheory make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 15%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/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 -DrdInfoTheory_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 15%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 15%] Built target rdAlignment make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/Data /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Data /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Data/CMakeFiles/cQuantize.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Data/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Data/CMakeFiles/cQuantize.dir/depend.internal". Scanning dependencies of target cQuantize make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 15%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Data && /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 -DcQuantize_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/Data/cQuantize.cpp [ 15%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/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 -DrdInfoTheory_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp [ 16%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2020.09.4 CMakeFiles/GraphMol.dir/Atom.cpp.o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o CMakeFiles/GraphMol.dir/QueryBond.cpp.o CMakeFiles/GraphMol.dir/Bond.cpp.o CMakeFiles/GraphMol.dir/MolOps.cpp.o CMakeFiles/GraphMol.dir/FindRings.cpp.o CMakeFiles/GraphMol.dir/ROMol.cpp.o CMakeFiles/GraphMol.dir/RWMol.cpp.o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o CMakeFiles/GraphMol.dir/atomic_data.cpp.o CMakeFiles/GraphMol.dir/QueryOps.cpp.o CMakeFiles/GraphMol.dir/MolPickler.cpp.o CMakeFiles/GraphMol.dir/Canon.cpp.o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o CMakeFiles/GraphMol.dir/BondIterators.cpp.o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o CMakeFiles/GraphMol.dir/Kekulize.cpp.o CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o CMakeFiles/GraphMol.dir/AddHs.cpp.o CMakeFiles/GraphMol.dir/Matrices.cpp.o CMakeFiles/GraphMol.dir/Chirality.cpp.o CMakeFiles/GraphMol.dir/RingInfo.cpp.o CMakeFiles/GraphMol.dir/Conformer.cpp.o CMakeFiles/GraphMol.dir/Renumber.cpp.o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o CMakeFiles/GraphMol.dir/Resonance.cpp.o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o CMakeFiles/GraphMol.dir/new_canon.cpp.o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o CMakeFiles/GraphMol.dir/FindStereo.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1 ../../lib/libRDKitGraphMol.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 16%] Built target GraphMol make -f 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Scanning dependencies of target testChemicalFeatures make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 16%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ChemicalFeatures/testChemicalFeatures.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/Data/cQuantize.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 16%] Linking CXX executable testChemicalFeatures cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -o testChemicalFeatures ../../lib/libRDKitChemicalFeatures.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 16%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/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 -DrdInfoTheory_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp [ 16%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so -lpthread make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 16%] Built target testChemicalFeatures make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ChemicalFeatures/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake --color= [ 16%] Built target cQuantize Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend.internal". make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolTransforms /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target rdChemicalFeatures make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend.internal". [ 16%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/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 -DrdChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp Scanning dependencies of target MolTransforms make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 16%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolTransforms_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolTransforms/MolTransforms.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 16%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/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 -DrdChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp [ 16%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o ../../../../lib/libRDKitInfoTheory.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 16%] Built target rdInfoTheory make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Substruct /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend.internal". Scanning dependencies of target SubstructMatch make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 16%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_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 -DSubstructMatch_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Substruct/SubstructMatch.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 16%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 16%] Built target MolTransforms [ 16%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_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 -DSubstructMatch_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Substruct/SubstructUtils.cpp [ 16%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdChemicalFeatures.so CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../../lib/libRDKitChemicalFeatures.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 16%] Built target rdChemicalFeatures make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend.internal". Scanning dependencies of target SmilesParse make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 16%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_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 -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesParse.cpp [ 17%] Linking CXX executable testConrec cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConrec.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testConrec.dir/testConrec.cpp.o -o testConrec ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 17%] Built target testConrec make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Trajectory /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend.internal". 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Scanning dependencies of target Subgraphs make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 17%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_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 -DSubgraphs_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Subgraphs/Subgraphs.cpp [ 17%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 17%] Built target SubstructMatch make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/PartialCharges /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend.internal". 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Scanning dependencies of target PartialCharges make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 18%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/PartialCharges/GasteigerCharges.cpp [ 18%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2020.09.4 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 18%] Built target Trajectory make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolTransforms/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend.internal". 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Scanning dependencies of target rdMolTransforms make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 18%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/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 -DrdMolTransforms_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp [ 18%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_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 -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesParseOps.cpp [ 18%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/PartialCharges/GasteigerParams.cpp [ 18%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_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 -DSubgraphs_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Subgraphs/SubgraphUtils.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 18%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 18%] Built target PartialCharges make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ShapeHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend.internal". 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Scanning dependencies of target MolCatalog make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 18%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp [ 18%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_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 -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesWrite.cpp [ 18%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_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 -DShapeHelpers_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp [ 19%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 19%] Built target rdMolTransforms make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend.internal". 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Scanning dependencies of target CIPLabeler make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 19%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/CIPMol.cpp [ 20%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolCatalog/MolCatalogParams.cpp [ 20%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2020.09.4 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2020.09.4 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 20%] Built target MolCatalog make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolInterchange /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend.internal". Scanning dependencies of target MolInterchange make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 20%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/rapidjson -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolInterchange.dir/Parser.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolInterchange/Parser.cpp [ 20%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/CIPLabeler.cpp [ 20%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2020.09.4 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2020.09.4 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 20%] Built target ShapeHelpers make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SLNParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend.internal". 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-I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SLNParse/SLNParse.cpp [ 20%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_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 -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/SmartsWrite.cpp [ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Mancude.cpp [ 21%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/rapidjson -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolInterchange.dir/Writer.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolInterchange/Writer.cpp [ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Digraph.cpp [ 21%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_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 -DSLNParse_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SLNParse/SLNAttribs.cpp [ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_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 -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/CXSmilesOps.cpp [ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Node.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Node.cpp [ 21%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2020.09.4 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2020.09.4 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 21%] Built target MolInterchange make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend.internal". Scanning dependencies of target rdqueries make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 22%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdqueries_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdqueries.dir/rdqueries.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/rdqueries.cpp [ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Edge.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Edge.cpp [ 22%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_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 -DSLNParse_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SLNParse/sln.tab.cpp [ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Sort.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Sort.cpp [ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Configuration.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/rdqueries.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 22%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdqueries_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/Queries.cpp [ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_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 -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/smarts.tab.cpp [ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp [ 22%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_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 -DSLNParse_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SLNParse/lex.yysln.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/Queries.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp [ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_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 -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/smiles.tab.cpp [ 22%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2020.09.4 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o CMakeFiles/SLNParse.dir/sln.tab.cpp.o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2020.09.4 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 22%] Built target SLNParse make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend.internal". Scanning dependencies of target rdtrajectory make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 22%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdtrajectory_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/Trajectory.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule2.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/Trajectory.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_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 -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/lex.yysmarts.cpp [ 24%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 24%] Built target rdqueries make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend.internal". Scanning dependencies of target MolAlign make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 24%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign/AlignMolecules.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule3.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp [ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdtrajectory_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/rdTrajectory.cpp [ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_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 -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/lex.yysmiles.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5.cpp [ 24%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2020.09.4 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl 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-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/rdTrajectory.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 24%] Built target MolAlign make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Optimizer /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend.internal". Scanning dependencies of target Optimizer make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 24%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Optimizer/BFGSOpt.cpp [ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp [ 25%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so -lpthread make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Built target rdtrajectory [ 25%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Optimizer/LinearSearch.cpp [ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule6.cpp [ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/PartialCharges/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu 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Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend.internal". Scanning dependencies of target rdPartialCharges make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/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 -DrdPartialCharges_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp [ 25%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2020.09.4 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Built target Optimizer make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ShapeHelpers/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend.internal". Scanning dependencies of target rdShapeHelpers make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/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 -DrdShapeHelpers_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp [ 25%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Built target SmilesParse make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolCatalog/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend.internal". Scanning dependencies of target rdMolCatalog make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/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 -DrdMolCatalog_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 25%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCIPLabeler.so.1 -o ../../../lib/libRDKitCIPLabeler.so.1.2020.09.4 CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o CMakeFiles/CIPLabeler.dir/Node.cpp.o CMakeFiles/CIPLabeler.dir/Edge.cpp.o CMakeFiles/CIPLabeler.dir/Sort.cpp.o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2020.09.4 ../../../lib/libRDKitCIPLabeler.so.1 ../../../lib/libRDKitCIPLabeler.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Built target CIPLabeler make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend.internal". Scanning dependencies of target testCIPLabeler make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/catch_tests.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.h:15, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp:5: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 25%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Built target rdPartialCharges make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend.internal". Scanning dependencies of target rdCIPLabeler make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Building CXX object Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/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 -DrdCIPLabeler_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Conformer.h:14, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ROMol.h:36, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp:13: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h: In function ‘boost::python::tuple RDKit::getUnionOfTwoBox(boost::python::tuple, boost::python::tuple)’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:58:31: warning: ‘*((void*)(&)+32).RDGeom::Point3D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:58:43: warning: ‘*((void*)(&)+32).RDGeom::Point3D::y’ may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:58:55: warning: ‘*((void*)(&)+32).RDGeom::Point3D::z’ may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:58:31: warning: ‘*((void*)(&)+32).RDGeom::Point3D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:58:43: warning: ‘*((void*)(&)+32).RDGeom::Point3D::y’ may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:58:55: warning: ‘*((void*)(&)+32).RDGeom::Point3D::z’ may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:58:31: warning: ‘*((void*)(&)+32).RDGeom::Point3D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:58:43: warning: ‘*((void*)(&)+32).RDGeom::Point3D::y’ may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:58:55: warning: ‘*((void*)(&)+32).RDGeom::Point3D::z’ may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:58:31: warning: ‘*((void*)(&)+32).RDGeom::Point3D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:58:43: warning: ‘*((void*)(&)+32).RDGeom::Point3D::y’ may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:58:55: warning: ‘*((void*)(&)+32).RDGeom::Point3D::z’ may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ 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-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp:13: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 25%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o ../../../../lib/libRDKitShapeHelpers.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Built target rdShapeHelpers make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ReducedGraphs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend.internal". Scanning dependencies of target ReducedGraphs make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_REDUCEDGRAPHS_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 -DReducedGraphs_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp [ 25%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o ../../../../lib/libRDKitCIPLabeler.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Built target rdCIPLabeler make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolInterchange/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend.internal". Scanning dependencies of target rdMolInterchange make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/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 -DrdMolInterchange_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/rapidjson -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp [ 25%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Built target rdMolCatalog make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SLNParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend.internal". Scanning dependencies of target testSLNParse make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSLNParse.dir/test.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SLNParse/test.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 25%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitReducedGraphs.so.1 -o ../../../lib/libRDKitReducedGraphs.so.1.2020.09.4 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitReducedGraphs.so.1.2020.09.4 ../../../lib/libRDKitReducedGraphs.so.1 ../../../lib/libRDKitReducedGraphs.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Built target ReducedGraphs make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SLNParse/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend.internal". Scanning dependencies of target rdSLNParse make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/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 -DrdSLNParse_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp [ 25%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolInterchange.so CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o ../../../../lib/libRDKitMolInterchange.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Built target rdMolInterchange [ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/CIPMol.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp:35: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Abbreviations /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend.internal". Scanning dependencies of target Abbreviations make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 25%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ABBREVIATIONS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Abbreviations/Abbreviations.cpp [ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 26%] Built target rdSLNParse make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend.internal". Scanning dependencies of target Depictor make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 26%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Depictor.dir/RDDepictor.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor/RDDepictor.cpp [ 26%] Linking CXX executable testSLNParse cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 26%] Built target testSLNParse [ 26%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor/EmbeddedFrag.cpp [ 26%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ABBREVIATIONS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp [ 26%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor/DepictUtils.cpp [ 26%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAbbreviations.so.1 -o ../../../lib/libRDKitAbbreviations.so.1.2020.09.4 CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2020.09.4 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 26%] Built target Abbreviations make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemTransforms 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemTransforms/ChemTransforms.cpp [ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/CIPLabeler.cpp [ 26%] Linking CXX shared library ../../../lib/libRDKitDepictor.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2020.09.4 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o ../../../lib/libRDKitMolAlign.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 26%] Built target Depictor make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 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Scanning dependencies of target testOptimizer make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 27%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Optimizer/testOptimizer.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/External/CoordGen/Wrap/rdCoordGen.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 27%] Linking CXX executable testOptimizer cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 27%] Built target testOptimizer [ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/Node.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Node.cpp make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu 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-O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/cptest.cpp [ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Edge.cpp [ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Sort.cpp [ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Configuration.cpp [ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/AngleBend.cpp [ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ 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Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend.internal". Scanning dependencies of target graphmolqueryTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 28%] Building CXX object Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/querytest.cpp [ 28%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 28%] Built target ChemTransforms make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/depend.internal". 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-g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/test-valgrind.cpp [ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/Nonbonded.cpp [ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/Inversion.cpp [ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -o test-valgrind ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 29%] Built target test-valgrind make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend.internal". 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/itertest.cpp [ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/TorsionAngle.cpp [ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp [ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule2.cpp [ 29%] Linking CXX executable graphmolIterTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -o graphmolIterTest ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory 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Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 30%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp [ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/TorsionConstraint.cpp [ 30%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp [ 30%] Linking CXX executable graphmolMemTest1 cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 30%] Built target graphmolMemTest1 make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 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Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend.internal". Scanning dependencies of target smaTest1 make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 30%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/smatest.cpp [ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/PositionConstraint.cpp [ 30%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp [ 30%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5.cpp [ 31%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 31%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 31%] Built target rdDepictor make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend.internal". 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/smiTest2.dir/test2.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/test2.cpp [ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/Params.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/Params.cpp [ 31%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule6.cpp [ 31%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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-I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/OopBend.cpp [ 36%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/Nonbonded.cpp [ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && 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-ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/AngleConstraint.cpp [ 36%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/TorsionConstraint.cpp [ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/AtomPairs.cpp [ 37%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ 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-I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/Params.cpp make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 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Scanning dependencies of target testSubgraphs2 make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 38%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSubgraphs2.dir/test2.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Subgraphs/test2.cpp [ 38%] Linking CXX shared library ../../lib/libRDKitForceField.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2020.09.4 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 38%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/MHFP.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MHFP.cpp cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2020.09.4 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 38%] Built target ForceField make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Subgraphs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake" is newer than depender 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Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend.internal". Scanning dependencies of target testSubgraphs1 make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 38%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSubgraphs1.dir/test1.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Subgraphs/test1.cpp [ 38%] Linking CXX executable testSubgraphs2 cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubgraphs2.dir/test2.cpp.o -o testSubgraphs2 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 38%] Built target testSubgraphs2 [ 38%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp [ 38%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ 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/build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp [ 38%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp [ 38%] Linking CXX executable testSubgraphs1 cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubgraphs1.dir/test1.cpp.o -o testSubgraphs1 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 38%] Built target testSubgraphs1 make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog 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Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend.internal". Scanning dependencies of target FragCatalog make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 38%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp [ 38%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.cpp [ 39%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp [ 39%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.cpp [ 39%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/FingerprintUtil.cpp [ 39%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatGenerator.cpp [ 39%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp [ 39%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp [ 39%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatParams.cpp [ 39%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp [ 39%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 39%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/FragFPGenerator.cpp cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 39%] Built target FilterCatalog make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/PartialCharges /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake" 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Scanning dependencies of target MolChemicalFeatures make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 39%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp [ 39%] Linking CXX executable testPartialCharges cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testPartialCharges.dir/test1.cpp.o -o testPartialCharges ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 39%] Built target testPartialCharges [ 39%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp [ 39%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2020.09.4 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o CMakeFiles/Fingerprints.dir/MHFP.cpp.o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 39%] Built target Fingerprints [ 39%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp [ 40%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2020.09.4 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2020.09.4 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 40%] Built target FragCatalog make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ReducedGraphs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend.internal". Scanning dependencies of target testReducedGraphs make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 40%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ReducedGraphs/test1.cpp [ 40%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ReducedGraphs/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend.internal". Scanning dependencies of target rdReducedGraphs make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 40%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/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 -DrdReducedGraphs_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend.internal". Scanning dependencies of target SubstructLibrary make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 40%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_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 -DSubstructLibrary_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp [ 41%] Linking CXX executable testReducedGraphs cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o testReducedGraphs ../../../lib/libRDKitReducedGraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 41%] Built target testReducedGraphs make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend.internal". Scanning dependencies of target rdchem make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 41%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/rdchem.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/rdchem.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp:13: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/rdchem.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 41%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2020.09.4 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2020.09.4 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 41%] Built target MolChemicalFeatures [ 42%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/Table.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/Table.cpp [ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 42%] Built target rdReducedGraphs make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Abbreviations/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend.internal". Scanning dependencies of target rdAbbreviations make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 42%] Building CXX object Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/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 -DrdAbbreviations_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/Table.cpp:13: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 42%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_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 -DSubstructLibrary_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary/PatternFactory.cpp [ 42%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/Atom.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/Atom.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/Atom.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 43%] Built target rdAbbreviations [ 43%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/Bond.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/Bond.cpp [ 44%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2020.09.4 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2020.09.4 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 44%] Built target SubstructLibrary make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend.internal". Scanning dependencies of target FileParsers make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/Mol2FileParser.cpp [ 44%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/Mol.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/Bond.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/Mol.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolFileParser.cpp [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupParsing.cpp [ 44%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/Conformer.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/Conformer.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h: In function ‘std::string RDKit::SGroupWriting::BuildV2000SAPLines(int, const RDKit::SubstanceGroup&)’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:25: warning: ‘%3d’ directive output may be truncated writing between 3 and 11 bytes into a region of size 4 [-Wformat-truncation=] 24 | snprintf(output, 5, " %3d", value); | ^~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: note: directive argument in the range [-2147483647, 2147483647] 24 | snprintf(output, 5, " %3d", value); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/streambuf:41, from /usr/include/c++/10/bits/streambuf_iterator.h:35, from /usr/include/c++/10/iterator:66, from /usr/include/boost/iterator/iterator_traits.hpp:10, from /usr/include/boost/range/mutable_iterator.hpp:23, from /usr/include/boost/range/iterator.hpp:20, from /usr/include/boost/range/begin.hpp:20, from /usr/include/boost/algorithm/string/detail/sequence.hpp:17, from /usr/include/boost/algorithm/string/join.hpp:15, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 5 and 13 bytes into a destination of size 5 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 44%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/RingInfo.cpp [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolFileStereochem.cpp [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolFileWriter.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/RingInfo.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp [ 45%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/EditableMol.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/EditableMol.cpp [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/SDMolSupplier.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/EditableMol.cpp:17: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/SDWriter.cpp [ 45%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/MonomerInfo.cpp [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp [ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/ResonanceMolSupplier.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/MonomerInfo.cpp:13: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/SmilesWriter.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp:15: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/TDTMolSupplier.cpp [ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/MolBundle.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/MolBundle.cpp [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/TDTWriter.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/TplFileParser.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-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/MolBundle.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 47%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/StereoGroup.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/StereoGroup.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/StereoGroup.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/TplFileWriter.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/PDBParser.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/PDBParser.cpp make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend.internal". Scanning dependencies of target ForceFieldHelpers make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 47%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp [ 47%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/SubstanceGroup.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/PDBWriter.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/SubstanceGroup.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 47%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/PDBSupplier.cpp [ 47%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/XYZFileWriter.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MaeMolSupplier.cpp In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Conformer.h:14, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RDKitBase.h:25, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/SubstanceGroup.cpp:17: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h: In function ‘void RDKit::{anonymous}::addBracketHelper(RDKit::SubstanceGroup&, boost::python::api::object)’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:58:31: warning: ‘*((void*)(&)+32).RDGeom::Point3D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:58:43: warning: ‘*((void*)(&)+32).RDGeom::Point3D::y’ may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:58:55: warning: ‘*((void*)(&)+32).RDGeom::Point3D::z’ may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ [ 47%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/Chirality.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/Chirality.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/ProximityBonds.cpp [ 47%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/SequenceParsers.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/Chirality.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 48%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp [ 48%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdchem.so CMakeFiles/rdchem.dir/rdchem.cpp.o CMakeFiles/rdchem.dir/Table.cpp.o CMakeFiles/rdchem.dir/Atom.cpp.o CMakeFiles/rdchem.dir/Bond.cpp.o CMakeFiles/rdchem.dir/Mol.cpp.o CMakeFiles/rdchem.dir/Conformer.cpp.o CMakeFiles/rdchem.dir/RingInfo.cpp.o CMakeFiles/rdchem.dir/EditableMol.cpp.o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o CMakeFiles/rdchem.dir/MolBundle.cpp.o CMakeFiles/rdchem.dir/StereoGroup.cpp.o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o CMakeFiles/rdchem.dir/Chirality.cpp.o ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/SequenceWriters.cpp make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 48%] Built target rdchem make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap 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Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend.internal". Scanning dependencies of target rdfiltercatalog make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 48%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/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 -Drdfiltercatalog_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp [ 49%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD 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/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/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 -Drdfiltercatalog_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.h:36, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp:32: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SVGParser.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/SVGParser.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp:31: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/PNGParser.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/PNGParser.cpp [ 49%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 49%] Built target ForceFieldHelpers make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend.internal". Scanning dependencies of target rdMHFPFingerprint make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 49%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/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 -DrdMHFPFingerprint_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.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-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend.internal". Scanning dependencies of target rdFingerprintGenerator make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/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 -DrdFingerprintGenerator_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp [ 50%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 50%] Built target rdMHFPFingerprint make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend.internal". Scanning dependencies of target rdForceFieldHelpers make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/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 -DrdForceFieldHelpers_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.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-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:13: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 50%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/FileParsers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFileParsers.so.1 -o ../../../lib/libRDKitFileParsers.so.1.2020.09.4 CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDWriter.cpp.o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o CMakeFiles/FileParsers.dir/PDBParser.cpp.o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o CMakeFiles/FileParsers.dir/SVGParser.cpp.o CMakeFiles/FileParsers.dir/PNGParser.cpp.o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1 ../../../lib/libRDKitFileParsers.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 50%] Built target FileParsers make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend.internal". Scanning dependencies of target O3AAlign make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DO3AAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign/O3AAlignMolecules.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 51%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 51%] Built target rdfiltercatalog make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend.internal". Scanning dependencies of target testFeatures make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 51%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp [ 51%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 51%] Built target rdFingerprintGenerator make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend.internal". Scanning dependencies of target rdMolChemicalFeatures make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/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 -DrdMolChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp [ 52%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 52%] Built target rdForceFieldHelpers make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ShapeHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend.internal". Scanning dependencies of target testShapeHelpers make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp [ 52%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2020.09.4 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2020.09.4 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 52%] Built target O3AAlign [ 52%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/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 -DrdMolChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 52%] Linking CXX executable testShapeHelpers cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 52%] Built target testShapeHelpers make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolCatalog /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend.internal". Scanning dependencies of target testMolCatalog make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolCatalog/test1.cpp [ 52%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/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 -DrdMolChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 52%] Linking CXX executable testFeatures cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFeatures.dir/testFeatures.cpp.o -o testFeatures ../../../lib/libRDKitMolChemicalFeatures.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 52%] Built target testFeatures make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend.internal". Scanning dependencies of target FMCS make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/FMCS.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /usr/include/boost/property_tree/json_parser/detail/parser.hpp:7, from /usr/include/boost/property_tree/json_parser/detail/read.hpp:13, from /usr/include/boost/property_tree/json_parser.hpp:16, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/FMCS.cpp:16: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 52%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/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 -DrdMolChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp [ 53%] Linking CXX executable testMolCatalog cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 53%] Built target testMolCatalog make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MMPA /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend.internal". Scanning dependencies of target MMPA make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMMPA_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MMPA_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MMPA.dir/MMPA.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MMPA/MMPA.cpp make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Trajectory /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend.internal". Scanning dependencies of target trajectoryTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Trajectory/trajectoryTest.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 53%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolChemicalFeatures.so CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o ../../../../lib/libRDKitMolChemicalFeatures.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 53%] Built target rdMolChemicalFeatures make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend.internal". Scanning dependencies of target substructLibraryTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp [ 53%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/Seed.cpp [ 54%] Linking CXX executable trajectoryTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 [ 54%] Linking CXX shared library ../../../lib/libRDKitMMPA.so /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2020.09.4 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 54%] Built target trajectoryTest make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake --color= 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Scanning dependencies of target rdSubstructLibrary make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2020.09.4 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so [ 54%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/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 -DrdSubstructLibrary_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 54%] Built target MMPA make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolInterchange /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend.internal". Scanning dependencies of target molInterchangeTest1 make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/rapidjson -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolInterchange/test1.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.h:36, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp:32: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 55%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/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 -DrdSubstructLibrary_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp [ 55%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp [ 55%] Linking CXX executable substructLibraryTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 55%] Built target substructLibraryTest make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend.internal". Scanning dependencies of target rdmolfiles make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/rdmolfiles.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp:31: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp:34: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/rdmolfiles.cpp:13: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 55%] Linking CXX executable molInterchangeTest1 cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -o molInterchangeTest1 ../../../lib/libRDKitMolInterchange.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 55%] Built target molInterchangeTest1 make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Abbreviations /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/depend.internal". Scanning dependencies of target testAbbreviations make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/__/catch_main.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testAbbreviations.dir/__/catch_main.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/catch_main.cpp [ 55%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/SubstructMatchCustom.cpp [ 55%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 55%] Built target rdSubstructLibrary [ 56%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp [ 57%] Linking CXX shared library ../../../lib/libRDKitFMCS.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2020.09.4 CMakeFiles/FMCS.dir/FMCS.cpp.o CMakeFiles/FMCS.dir/Seed.cpp.o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2020.09.4 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 57%] Built target FMCS make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/External/CoordGen /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/depend.internal". Scanning dependencies of target testCoordGen make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 57%] Building CXX object External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCoordGen.dir/test.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/External/CoordGen/test.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:13: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:22: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend.internal". Scanning dependencies of target testUFFForceField make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 58%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/testUFFForceField.cpp [ 58%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/MaeMolSupplier.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/MaeMolSupplier.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 58%] Linking CXX executable testCoordGen cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoordGen.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCoordGen.dir/test.cpp.o -o testCoordGen /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl -lpthread make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 58%] Built target testCoordGen make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/depend.internal". Scanning dependencies of target DistGeometry make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 58%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/DistGeomUtils.cpp In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/MaeMolSupplier.cpp:22: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ [ 58%] Linking CXX executable testUFFForceField cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 58%] Built target testUFFForceField make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend.internal". Scanning dependencies of target rdForceField make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 58%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/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 -DrdForceField_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/Wrap/ForceField.cpp [ 58%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/SDMolSupplier.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/Wrap/ForceField.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 58%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/TriangleSmooth.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/SDMolSupplier.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 58%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/DistViolationContrib.cpp [ 58%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Abbreviations/catch_tests.cpp [ 59%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/ChiralViolationContrib.cpp [ 59%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/TDTMolSupplier.cpp [ 59%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2020.09.4 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../lib/libRDKitForceField.so.1.2020.09.4 ../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 59%] Built target DistGeometry make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol 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Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend.internal". Scanning dependencies of target chiralityTestsCatch make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 59%] Building CXX object Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/catch_chirality.cpp [ 59%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 59%] Built target rdForceField make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend.internal". Scanning dependencies of target graphmolSGroupCatch make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 59%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/catch_sgroups.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/TDTMolSupplier.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 59%] Linking CXX executable testAbbreviations cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAbbreviations.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAbbreviations.dir/__/catch_main.cpp.o CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -o testAbbreviations ../../../lib/libRDKitAbbreviations.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 59%] Built target testAbbreviations make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend.internal". Scanning dependencies of target graphmolTestsCatch make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 59%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/catch_graphmol.cpp [ 59%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/SmilesMolSupplier.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/SmilesMolSupplier.cpp:13: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 59%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_main.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolSGroupCatch.dir/catch_main.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/catch_main.cpp [ 59%] Building CXX object Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_main.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/chiralityTestsCatch.dir/catch_main.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/catch_main.cpp [ 59%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/SmilesWriter.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/SmilesWriter.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/SmilesWriter.cpp:20: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ [ 59%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_main.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolTestsCatch.dir/catch_main.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/catch_main.cpp [ 59%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/SDWriter.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/SDWriter.cpp:13: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/SDWriter.cpp:21: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ [ 59%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/TDTWriter.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/TDTWriter.cpp:13: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/TDTWriter.cpp:21: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ [ 60%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/PDBWriter.cpp [ 60%] Linking CXX executable graphmolSGroupCatch cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o CMakeFiles/graphmolSGroupCatch.dir/catch_main.cpp.o -o graphmolSGroupCatch ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/PDBWriter.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 60%] Built target graphmolSGroupCatch make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/depend.internal". Scanning dependencies of target testSGroup make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSGroup.dir/testSGroup.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/testSGroup.cpp In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/PDBWriter.cpp:20: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ [ 60%] Linking CXX executable chiralityTestsCatch cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o CMakeFiles/chiralityTestsCatch.dir/catch_main.cpp.o -o chiralityTestsCatch ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 60%] Built target chiralityTestsCatch make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend.internal". Scanning dependencies of target graphmolAdjustQueryCatch make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/catch_adjustquery.cpp [ 60%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp:13: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedMolSupplier.h:15, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp:23: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ [ 61%] Linking CXX executable graphmolTestsCatch cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o CMakeFiles/graphmolTestsCatch.dir/catch_main.cpp.o -o graphmolTestsCatch ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 61%] Built target graphmolTestsCatch make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend.internal". Scanning dependencies of target graphmoltestPicklerGlobalSetting make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/testPicklerGlobalSettings.cpp [ 61%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/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 -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp [ 62%] Building CXX object Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_main.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_main.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/catch_main.cpp [ 62%] Linking CXX executable testSGroup cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSGroup.dir/testSGroup.cpp.o -o testSGroup ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 62%] Built target testSGroup make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend.internal". Scanning dependencies of target graphmoltestChirality make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 62%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/testChirality.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp:13: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedMolSupplier.h:15, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp:23: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ [ 62%] Linking CXX executable graphmoltestPicklerGlobalSetting cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 62%] Built target graphmoltestPicklerGlobalSetting make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend.internal". Scanning dependencies of target graphmolTest1 make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 62%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/test1.cpp [ 62%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolfiles.so CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so -lpthread make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 62%] Built target rdmolfiles make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend.internal". Scanning dependencies of target resMolSupplierTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 62%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/resMolSupplierTest.cpp [ 63%] Linking CXX executable resMolSupplierTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 63%] Built target resMolSupplierTest make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend.internal". Scanning dependencies of target graphmoltestPickler make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 63%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/testPickler.cpp [ 63%] Linking CXX executable graphmolTest1 cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolTest1.dir/test1.cpp.o -o graphmolTest1 ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../lib/libRDKitForceField.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl -lpthread make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 63%] Built target graphmolTest1 make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend.internal". Scanning dependencies of target graphmolMolOpsTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 63%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/molopstest.cpp [ 63%] Linking CXX executable graphmoltestChirality cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 63%] Built target graphmoltestChirality make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/depend.internal". Scanning dependencies of target hanoiTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 63%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/hanoitest.cpp [ 63%] Linking CXX executable hanoiTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 63%] Built target hanoiTest make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/depend.internal". Scanning dependencies of target molBundleTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 64%] Building CXX object Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/testMolBundle.cpp [ 64%] Linking CXX executable graphmolAdjustQueryCatch cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolAdjustQueryCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_main.cpp.o -o graphmolAdjustQueryCatch ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 64%] Built target graphmolAdjustQueryCatch make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend.internal". Scanning dependencies of target testDepictor make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 64%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testDepictor.dir/testDepictor.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor/testDepictor.cpp [ 65%] Linking CXX executable graphmoltestPickler cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 65%] Built target graphmoltestPickler make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend.internal". Scanning dependencies of target smiTest1 make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/test.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/smiTest1.dir/test.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/test.cpp [ 65%] Linking CXX executable molBundleTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -o molBundleTest ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 65%] Built target molBundleTest make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend.internal". Scanning dependencies of target smiTestCatch make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/catch_tests.cpp [ 65%] Linking CXX executable testDepictor cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 65%] Built target testDepictor make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend.internal". Scanning dependencies of target cxsmilesTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 66%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/cxsmiles_test.cpp [ 66%] Linking CXX executable cxsmilesTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 66%] Built target cxsmilesTest make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend.internal". Scanning dependencies of target testMolWriter make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 67%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/testMolWriter.cpp [ 67%] Linking CXX executable smiTest1 cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 67%] Built target smiTest1 make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend.internal". Scanning dependencies of target testSequence make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 68%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/testSequence.cpp [ 68%] Linking CXX executable testSequence cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSequence.dir/testSequence.cpp.o -o testSequence ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 68%] Built target testSequence make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend.internal". Scanning dependencies of target fileParsersTest1 make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 68%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/test1.cpp [ 68%] Linking CXX executable testMolWriter cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 68%] Built target testMolWriter make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend.internal". Scanning dependencies of target testMolSupplier make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 68%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/testMolSupplier.cpp [ 69%] Linking CXX executable graphmolMolOpsTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 69%] Built target graphmolMolOpsTest make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/depend.internal". Scanning dependencies of target testMultithreadedMolSupplier make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 69%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/testMolSupplier.cpp: In function ‘void testGitHub3517()’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/testMolSupplier.cpp:2805:10: warning: unused variable ‘l’ [-Wunused-variable] 2805 | size_t l = sdsup.length(); | ^ [ 69%] Linking CXX executable testMultithreadedMolSupplier cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitRDStreams.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl -lpthread /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 69%] Built target testMultithreadedMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend.internal". Scanning dependencies of target testExtendedStereoParsing make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 69%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp [ 70%] Linking CXX executable testExtendedStereoParsing cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 70%] Built target testExtendedStereoParsing make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend.internal". Scanning dependencies of target testGeneralFileReader make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 70%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/testGeneralFileReader.cpp [ 70%] Linking CXX executable smiTestCatch cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 70%] Built target smiTestCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend.internal". Scanning dependencies of target testTplParser make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 70%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testTplParser.dir/testTpls.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/testTpls.cpp [ 70%] Linking CXX executable testMolSupplier cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitRDStreams.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -lpthread /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 70%] Built target testMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend.internal". Scanning dependencies of target testMol2ToMol make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 70%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/testMol2ToMol.cpp [ 71%] Linking CXX executable testGeneralFileReader cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitRDStreams.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -lpthread /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 71%] Built target testGeneralFileReader make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend.internal". Scanning dependencies of target fileParsersCatchTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 71%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/file_parsers_catch.cpp [ 71%] Linking CXX executable testTplParser cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 71%] Built target testTplParser make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend.internal". Scanning dependencies of target testPropertyLists make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 71%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/testPropertyLists.cpp [ 71%] Linking CXX executable testMol2ToMol cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 71%] Built target testMol2ToMol [ 71%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/catch_main.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testPropertyLists.dir/catch_main.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/catch_main.cpp [ 72%] Linking CXX executable fileParsersTest1 cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 72%] Built target fileParsersTest1 [ 72%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/catch_main.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/fileParsersCatchTest.dir/catch_main.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/catch_main.cpp make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Substruct /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend.internal". Scanning dependencies of target testSubstructMatch make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 72%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Substruct/test1.cpp make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Substruct /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend.internal". Scanning dependencies of target substructTestCatch make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 72%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Substruct/catch_tests.cpp [ 72%] Linking CXX executable testSubstructMatch cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 72%] Built target testSubstructMatch make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend.internal". 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Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend.internal". Scanning dependencies of target testChemTransforms make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 73%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemTransforms/testChemTransforms.cpp [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/BCUT.cpp [ 73%] Linking CXX executable fileParsersCatchTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o CMakeFiles/fileParsersCatchTest.dir/catch_main.cpp.o -o fileParsersCatchTest ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 73%] Built target fileParsersCatchTest make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemTransforms /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend.internal". Scanning dependencies of target chemTransformsTestCatch make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 73%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemTransforms/catch_tests.cpp [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 73%] Built target testChemTransforms make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 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Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend.internal". Scanning dependencies of target filterCatalogTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 73%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/MolSurf.cpp [ 73%] Linking CXX executable substructTestCatch cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 73%] Built target substructTestCatch [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/Lipinski.cpp make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd 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Scanning dependencies of target testFragCatalog make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 73%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/test1.cpp [ 73%] Linking CXX executable filterCatalogTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 73%] Built target filterCatalogTest make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend.internal". Scanning dependencies of target rdfragcatalog make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 73%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/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 -Drdfragcatalog_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/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-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.h:15, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 73%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/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 -Drdfragcatalog_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp [ 73%] Linking CXX executable testFragCatalog cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 73%] Built target testFragCatalog make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend.internal". Scanning dependencies of target testMHFPFingerprint make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 73%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/testMHFPFingerprint.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/MQN.cpp [ 73%] Linking CXX executable testMHFPFingerprint cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -o testMHFPFingerprint ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/Property.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/Property.cpp [ 74%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/AUTOCORR2D.cpp [ 74%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/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 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/build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp [ 74%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/MolData3Ddescriptors.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 74%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/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 -Drdfragcatalog_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp [ 74%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/USRDescriptor.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 74%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/AtomFeat.cpp [ 74%] Linking CXX executable chemTransformsTestCatch cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemTransformsTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -o chemTransformsTestCatch ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 74%] Built target chemTransformsTestCatch make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend.internal". Scanning dependencies of target testFingerprintGenerators make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 74%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp [ 74%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/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 -Drdfragcatalog_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend.internal". Scanning dependencies of target fpTestCatch make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 74%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/catch_tests.cpp [ 74%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/EEM.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/EEM.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 74%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfragcatalog.so CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o ../../../../lib/libRDKitFragCatalog.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 74%] Built target rdfragcatalog make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend.internal". Scanning dependencies of target testFingerprints make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 74%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/test1.cpp [ 74%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/PBF.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/PBF.cpp [ 75%] Linking CXX executable testFingerprintGenerators cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 75%] Built target testFingerprintGenerators make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 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Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend.internal". Scanning dependencies of target testMolTransforms make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 75%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolTransforms.dir/test1.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolTransforms/test1.cpp [ 76%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/PMI.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/PMI.cpp [ 76%] Linking CXX executable testMolTransforms cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. 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Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend.internal". Scanning dependencies of target testFMCS make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 76%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/testFMCS_Unit.cpp [ 76%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/AUTOCORR3D.cpp [ 76%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/RDF.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/RDF.cpp [ 76%] Linking CXX executable testFingerprints cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 76%] Built target testFingerprints make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 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Scanning dependencies of target rdFMCS make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 76%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/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 -DrdFMCS_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp [ 76%] Linking CXX executable testFMCS cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFMCS.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 76%] Built target testFMCS make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/Test /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend.internal". Scanning dependencies of target FMCStest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 76%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/FMCStest.dir/testFMCS.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/Test/testFMCS.cpp [ 76%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/MORSE.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/MORSE.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 76%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/GETAWAY.cpp [ 76%] Linking CXX executable fpTestCatch cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -o fpTestCatch ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 76%] Built target fpTestCatch make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MMPA /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend.internal". Scanning dependencies of target testMMPA make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 76%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MMPA/MMPA_UnitTest.cpp [ 76%] Linking CXX executable FMCStest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/FMCStest.dir/testFMCS.cpp.o -o FMCStest ../../../../lib/libRDKitFMCS.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 76%] Built target FMCStest make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MMPA/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend.internal". Scanning dependencies of target rdMMPA make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 77%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/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 -DrdMMPA_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MMPA/Wrap/rdMMPA.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-TKP8Bz/rdkit-202009.4/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 77%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 77%] Built target rdFMCS make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend.internal". 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Scanning dependencies of target RGroupDecomposition make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 77%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_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 -DRGroupDecomposition_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp [ 77%] Linking CXX executable testMMPA cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMPA.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -o testMMPA ../../../lib/libRDKitMMPA.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 77%] Built target testMMPA make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/DistGeomHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend.internal". Scanning dependencies of target DistGeomHelpers make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 77%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp [ 77%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 77%] Built target rdMMPA make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/depend.internal". Scanning dependencies of target testDistGeom make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 77%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/testDistGeom.cpp [ 78%] Linking CXX executable testDistGeom cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../lib/libRDKitForceField.so.1.2020.09.4 ../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 78%] Built target testDistGeom make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend.internal". 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Scanning dependencies of target DistGeom make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 79%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeom_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/Wrap/DistGeom.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/Wrap/DistGeom.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 79%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/Embedder.cpp [ 79%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 79%] Built target DistGeom [ 79%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o cd 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-c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp [ 79%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_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 -DRGroupDecomposition_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security 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-I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/WHIM.cpp [ 79%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_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 -DRGroupDecomposition_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupScore.cpp [ 79%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 79%] Built target DistGeomHelpers make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 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Scanning dependencies of target testMMFFForceField make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 79%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/MMFF && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/testMMFFForceField.cpp make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend.internal". 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Scanning dependencies of target testMMFFForceFieldHelpersMultiThread make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 79%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp [ 80%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2020.09.4 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o ../../../lib/libRDKitFMCS.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2020.09.4 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 80%] Built target RGroupDecomposition [ 80%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/CoulombMat.cpp [ 80%] Linking CXX executable testMMFFForceFieldHelpersMultiThread cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o testMMFFForceFieldHelpersMultiThread ../../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 80%] Built target testMMFFForceFieldHelpersMultiThread make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend.internal". Scanning dependencies of target testMMFFForceFieldHelpers make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 80%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend.internal". Scanning dependencies of target testUFFForceFieldHelpers make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 80%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp [ 80%] Linking CXX executable testMMFFForceField cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 80%] Built target testMMFFForceField make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend.internal". Scanning dependencies of target testCrystalForceField make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 80%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp [ 80%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2020.09.4 CMakeFiles/Descriptors.dir/Crippen.cpp.o CMakeFiles/Descriptors.dir/BCUT.cpp.o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o CMakeFiles/Descriptors.dir/MolSurf.cpp.o CMakeFiles/Descriptors.dir/Lipinski.cpp.o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o CMakeFiles/Descriptors.dir/MQN.cpp.o CMakeFiles/Descriptors.dir/Property.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o CMakeFiles/Descriptors.dir/EEM.cpp.o CMakeFiles/Descriptors.dir/PBF.cpp.o CMakeFiles/Descriptors.dir/PMI.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o CMakeFiles/Descriptors.dir/RDF.cpp.o CMakeFiles/Descriptors.dir/MORSE.cpp.o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o CMakeFiles/Descriptors.dir/WHIM.cpp.o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 80%] Built target Descriptors make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/DistGeomHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend.internal". Scanning dependencies of target testDistGeomHelpers make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 80%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp [ 81%] Linking CXX executable testMMFFForceFieldHelpers cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 81%] Built target testMMFFForceFieldHelpers make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend.internal". Scanning dependencies of target rdDistGeom make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 81%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_PYTHON_MAX_ARITY=32 -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 -DrdDistGeom_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp [ 81%] Linking CXX executable testUFFForceFieldHelpers cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 [ 81%] Linking CXX executable testCrystalForceField cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 81%] Built target testCrystalForceField make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend.internal". make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' Scanning dependencies of target testO3AAlign [ 81%] Built target testUFFForceFieldHelpers make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend.internal". [ 81%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign/testO3AAlign.cpp Scanning dependencies of target testMolAlign make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 81%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign/testMolAlign.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 81%] Linking CXX executable testMolAlign cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 81%] Built target testMolAlign make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend.internal". Scanning dependencies of target rdMolAlign make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 81%] Building CXX object Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/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 -DrdMolAlign_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign/Wrap/rdMolAlign.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:14: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 81%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 81%] Linking CXX executable testO3AAlign cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 81%] Built target rdDistGeom make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolHash /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend.internal". Scanning dependencies of target MolHash make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 81%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolHash/hashfunctions.cpp make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 81%] Built target testO3AAlign make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend.internal". Scanning dependencies of target testRGroupDecomp make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 81%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp [ 81%] Linking CXX executable testDistGeomHelpers cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 81%] Built target testDistGeomHelpers make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend.internal". Scanning dependencies of target rdRGroupDecomposition make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 81%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/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 -DrdRGroupDecomposition_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp [ 82%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolHash.dir/normalize.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolHash/normalize.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp:32: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp:47: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ [ 82%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 82%] Built target rdMolAlign make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend.internal". Scanning dependencies of target ChemReactions make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 82%] Linking CXX executable testRGroupDecomp cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 [ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/Reaction.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Reaction.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2020.09.4 ../../../lib/libRDKitFMCS.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 83%] Built target testRGroupDecomp [ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/MDLParser.cpp [ 83%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2020.09.4 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2020.09.4 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 83%] Built target MolHash make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend.internal". Scanning dependencies of target testCoulombMat make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 83%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/testCoulombMat.cpp [ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitFMCS.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 83%] Built target rdRGroupDecomposition make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend.internal". Scanning dependencies of target testAUTOCORR3D make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 83%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/testAUTOCORR3D.cpp [ 83%] Linking CXX executable testCoulombMat cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 83%] Built target testCoulombMat [ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionWriter.cpp [ 83%] Linking CXX executable testMORSE cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMORSE.dir/link.txt --verbose=1 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Scanning dependencies of target testAUTOCORR2D make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 83%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/testAUTOCORR2D.cpp [ 83%] Linking CXX executable testGETAWAY cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGETAWAY.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -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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../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 83%] Built target testGETAWAY [ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionDepict.cpp [ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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Scanning dependencies of target testATF make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 84%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testATF.dir/testATF.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/testATF.cpp [ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_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 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-I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testEEM.dir/testEEM.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/testEEM.cpp [ 85%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_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 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executable testEEM cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEEM.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testEEM.dir/testEEM.cpp.o -o testEEM ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp [ 85%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp [ 85%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 86%] Linking CXX executable test3D cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/test3D.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/test3D.dir/test3D.cpp.o -o test3D ../../../lib/libRDKitDescriptors.so.1.2020.09.4 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../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 86%] Built target test3D make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/DependInfo.cmake" is 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Scanning dependencies of target rdMolDescriptors make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 87%] Building CXX object Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/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 -DrdMolDescriptors_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp [ 87%] Linking CXX executable testRDF cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDF.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDF.dir/testRDF.cpp.o -o testRDF ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 87%] Built target testRDF make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend.internal". 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Scanning dependencies of target MolDraw2D make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.cpp [ 87%] Linking CXX executable testRDFcustom cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDFcustom.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -o testRDFcustom ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 87%] Built target testRDFcustom make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolHash /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend.internal". Scanning dependencies of target molHashCatchTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 87%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolHash/catch_tests.cpp [ 87%] Linking CXX executable testWHIM cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testWHIM.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testWHIM.dir/testWHIM.cpp.o -o testWHIM ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 87%] Built target testWHIM make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolHash/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend.internal". Scanning dependencies of target rdMolHash make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 87%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/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 -DrdMolHash_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 87%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 87%] Built target rdMolHash [ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Conformer.h:14, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ROMol.h:36, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/GraphMol.h:19, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:12: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h: In function ‘boost::python::list {anonymous}::GetUSRDistributionsFromPoints(boost::python::api::object, boost::python::api::object)’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:87:15: warning: ‘*((void*)(&)+32).RDGeom::Point3D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 87 | x = other.x; | ~~~~~~^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:88:15: warning: ‘*((void*)(&)+32).RDGeom::Point3D::y’ may be used uninitialized in this function [-Wmaybe-uninitialized] 88 | y = other.y; | ~~~~~~^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:89:15: warning: ‘*((void*)(&)+32).RDGeom::Point3D::z’ may be used uninitialized in this function [-Wmaybe-uninitialized] 89 | z = other.z; | ~~~~~~^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h: In function ‘boost::python::list {anonymous}::GetUSRDistributions(boost::python::api::object, boost::python::api::object)’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:87:15: warning: ‘*((void*)(&)+32).RDGeom::Point3D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 87 | x = other.x; | ~~~~~~^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:88:15: warning: ‘*((void*)(&)+32).RDGeom::Point3D::y’ may be used uninitialized in this function [-Wmaybe-uninitialized] 88 | y = other.y; | ~~~~~~^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:89:15: warning: ‘*((void*)(&)+32).RDGeom::Point3D::z’ may be used uninitialized in this function [-Wmaybe-uninitialized] 89 | z = other.z; | ~~~~~~^ [ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp [ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DUtils.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-TKP8Bz/rdkit-202009.4/Code/Numerics/Vector.h:23, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:24, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:28, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawText.cpp [ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp [ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp [ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextJS.cpp [ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFT.cpp [ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp [ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTJS.cpp make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Deprotect /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend.internal". Scanning dependencies of target Deprotect make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 89%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDeprotect_EXPORTS -DRDKIT_DEPROTECT_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Deprotect/Deprotect.cpp [ 89%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 89%] Built target rdMolDescriptors make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend.internal". Scanning dependencies of target MolEnumerator make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 89%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.cpp [ 89%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolDraw2D.so.1 -o ../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o ../../../lib/libRDKitChemReactions.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 89%] Built target MolDraw2D make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend.internal". Scanning dependencies of target testReaction make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 89%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testReaction.dir/testReaction.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/testReaction.cpp [ 89%] Linking CXX executable molHashCatchTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../../lib/libRDKitMolHash.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 89%] Built target molHashCatchTest make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend.internal". Scanning dependencies of target testReactionFingerprints make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 89%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp [ 90%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/Deprotect.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDeprotect.so.1 -o ../../../lib/libRDKitDeprotect.so.1.2020.09.4 CMakeFiles/Deprotect.dir/Deprotect.cpp.o ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDeprotect.so.1.2020.09.4 ../../../lib/libRDKitDeprotect.so.1 ../../../lib/libRDKitDeprotect.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 90%] Built target Deprotect make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend.internal". Scanning dependencies of target testEnumeration make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 90%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp [ 90%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/PositionVariation.cpp [ 90%] Linking CXX executable testReactionFingerprints cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -o testReactionFingerprints ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 90%] Built target testReactionFingerprints make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend.internal". Scanning dependencies of target rxnTestCatch make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 90%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/catch_tests.cpp [ 90%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/LinkNode.cpp [ 90%] Linking CXX executable testEnumeration cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 90%] Built target testEnumeration make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend.internal". Scanning dependencies of target rdChemReactions make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 90%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/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 -DrdChemReactions_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.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-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 90%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2020.09.4 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2020.09.4 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 90%] Built target MolEnumerator make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend.internal". Scanning dependencies of target MolStandardize make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/MolStandardize.cpp [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Metal.cpp [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Normalize.cpp [ 91%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/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 -DrdChemReactions_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.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-TKP8Bz/rdkit-202009.4/Code/Numerics/Vector.h:23, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:24, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolPickler.h:14, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:32: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Validate.cpp [ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Charge.cpp [ 92%] Linking CXX executable testReaction cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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/usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 92%] Built target testReaction make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend.internal". Scanning dependencies of target moldraw2DRxnTest1 make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/rxn_test1.cpp [ 92%] Linking CXX executable rxnTestCatch cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/rxnTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -o rxnTestCatch ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 92%] Built target rxnTestCatch make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend.internal". Scanning dependencies of target moldraw2DTestCatch make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_main.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/moldraw2DTestCatch.dir/catch_main.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/catch_main.cpp [ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Tautomer.cpp [ 92%] Linking CXX executable moldraw2DRxnTest1 cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libfreetype.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 92%] Built target moldraw2DRxnTest1 [ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Fragment.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Fragment.cpp [ 92%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 92%] Built target rdChemReactions make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend.internal". Scanning dependencies of target moldraw2DTest1 make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 93%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/test1.cpp [ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend.internal". Scanning dependencies of target rdMolDraw2D make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 93%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDraw2D_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp [ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp [ 93%] Linking CXX executable moldraw2DTest1 cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libfreetype.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 93%] Built target moldraw2DTest1 make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Deprotect /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/depend.internal". Scanning dependencies of target deprotectTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 93%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Deprotect/deprotectTest.cpp [ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Conformer.h:14, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ROMol.h:36, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:17: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h: In function ‘std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = RDGeom::Point2D]’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:269:57: warning: ‘*((void*)(&)+32).RDGeom::Point2D::x’ may be used uninitialized in this function [-Wmaybe-uninitialized] 269 | Point2D(const Point2D &other) : Point(other), x(other.x), y(other.y) {} | ~~~~~~^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:269:69: warning: ‘*((void*)(&)+32).RDGeom::Point2D::y’ may be used uninitialized in this function [-Wmaybe-uninitialized] 269 | Point2D(const Point2D &other) : Point(other), x(other.x), y(other.y) {} | ~~~~~~^ [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp [ 94%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/catch_tests.cpp [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp [ 95%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libfreetype.so /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 95%] Built target rdMolDraw2D make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Deprotect/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/depend.internal". Scanning dependencies of target rdDeprotect make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 95%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_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 -DrdDeprotect_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Deprotect/Wrap/rdDeprotect.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Deprotect/Wrap/rdDeprotect.h:15, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 95%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_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 -DrdDeprotect_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp [ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g 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Scanning dependencies of target rdmolops make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 95%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/rdmolops.cpp [ 95%] Linking CXX executable moldraw2DTestCatch cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTestCatch.dir/catch_main.cpp.o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 ../../../lib/libRDKitCIPLabeler.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 95%] Built target moldraw2DTestCatch make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend.internal". Scanning dependencies of target testMolEnumerator make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 95%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/catch_main.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolEnumerator.dir/catch_main.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/catch_main.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/rdmolops.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 95%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/MolOps.cpp [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/MolOps.cpp:12: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/MolOps.cpp:30: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function ‘virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: ‘boost_adaptbx::python::streambuf::int_type’ {aka ‘int’} and ‘const unsigned int’ [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ [ 95%] Linking CXX executable deprotectTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/deprotectTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -o deprotectTest ../../../lib/libRDKitDeprotect.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 95%] Built target deprotectTest [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp [ 95%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/enumerator_catch.cpp [ 96%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolStandardize.so.1 -o ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o CMakeFiles/MolStandardize.dir/Metal.cpp.o CMakeFiles/MolStandardize.dir/Normalize.cpp.o CMakeFiles/MolStandardize.dir/Validate.cpp.o CMakeFiles/MolStandardize.dir/Charge.cpp.o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o CMakeFiles/MolStandardize.dir/Fragment.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 96%] Built target MolStandardize [ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/ChiralityOps.cpp make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend.internal". Scanning dependencies of target rdMolEnumerator make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 96%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/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 -DrdMolEnumerator_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap/ChiralityOps.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 96%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolEnumerator.so CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o ../../../../lib/libRDKitMolEnumerator.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 96%] Built target rdMolEnumerator make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/TautomerQuery /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend.internal". Scanning dependencies of target TautomerQuery make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 96%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TAUTOMERQUERY_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 -DTautomerQuery_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/TautomerQuery/TautomerQuery.cpp make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend.internal". Scanning dependencies of target molStandardizeTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molStandardizeTest.dir/test1.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/test1.cpp [ 97%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o ../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libfreetype.so /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Built target rdmolops make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend.internal". Scanning dependencies of target molNormalizeTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/testNormalize.cpp [ 97%] Linking CXX executable testMolEnumerator cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolEnumerator.dir/catch_main.cpp.o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../../lib/libRDKitMolEnumerator.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Built target testMolEnumerator make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend.internal". Scanning dependencies of target molValidateTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molValidateTest.dir/testValidate.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/testValidate.cpp [ 97%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2020.09.4 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2020.09.4 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Built target TautomerQuery make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend.internal". Scanning dependencies of target molChargeTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molChargeTest.dir/testCharge.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/testCharge.cpp [ 97%] Linking CXX executable molNormalizeTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -o molNormalizeTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Built target molNormalizeTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend.internal". Scanning dependencies of target molFragmentTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/testFragment.cpp [ 97%] Linking CXX executable molValidateTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Built target molValidateTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend.internal". Scanning dependencies of target molTautomerTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/testTautomer.cpp [ 97%] Linking CXX executable molStandardizeTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Built target molStandardizeTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend.internal". Scanning dependencies of target molStandardizeCatchTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/catch_tests.cpp [ 97%] Linking CXX executable molFragmentTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -o molFragmentTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Built target molFragmentTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend.internal". Scanning dependencies of target molStandardizeSmallTest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Linking CXX executable molChargeTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 [ 97%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/test2.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Built target molChargeTest make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend.internal". Scanning dependencies of target rdMolStandardize make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/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 -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 97%] Linking CXX executable molStandardizeSmallTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeSmallTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -o molStandardizeSmallTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Built target molStandardizeSmallTest make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend.internal". Scanning dependencies of target ScaffoldNetwork make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SCAFFOLDNETWORK_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 -DScaffoldNetwork_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp [ 99%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/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 -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Validate.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Validate.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 99%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitScaffoldNetwork.so.1 -o ../../../lib/libRDKitScaffoldNetwork.so.1.2020.09.4 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2020.09.4 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 99%] Built target ScaffoldNetwork make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/TautomerQuery /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend.internal". Scanning dependencies of target tautomerQueryTestCatch make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 99%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/TautomerQuery/catch_tests.cpp [ 99%] Linking CXX executable molTautomerTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 99%] Built target molTautomerTest make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/TautomerQuery/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend.internal". Scanning dependencies of target rdTautomerQuery make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 99%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/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 -DrdTautomerQuery_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp [ 99%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/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 -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Charge.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp:13: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Charge.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 99%] Built target rdTautomerQuery make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend.internal". Scanning dependencies of target testScaffoldNetwork make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 99%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_main.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testScaffoldNetwork.dir/catch_main.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/catch_main.cpp [ 99%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/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 -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Fragment.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-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 99%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/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 -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp [ 99%] Linking CXX executable molStandardizeCatchTest cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -o molStandardizeCatchTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl 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-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 99%] Built target molStandardizeCatchTest [ 99%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/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 -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Metal.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/Wrap.h:20, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Metal.cpp:10: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 99%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/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 -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake --color= Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend.internal". Dependee "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend.internal". Scanning dependencies of target rdScaffoldNetwork make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 99%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/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 -DrdScaffoldNetwork_EXPORTS -I/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object/class.hpp:9, from /usr/include/boost/python/class.hpp:13, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:9, from /usr/include/boost/python/suite/indexing/map_indexing_suite.hpp:9, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:11: /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ 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-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp:11: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: ‘#pragma message: This header is deprecated. Use instead.’ 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable tautomerQueryTestCatch cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/tautomerQueryTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../../lib/libRDKitTautomerQuery.so.1.2020.09.4 ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [100%] Built target tautomerQueryTestCatch [100%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /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/usr/include/catch2 -I/build/rdkit-TKP8Bz/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -I/build/rdkit-TKP8Bz/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/catch_tests.cpp [100%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o ../../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [100%] Built target rdMolStandardize [100%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o ../../../../lib/libRDKitScaffoldNetwork.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [100%] Built target rdScaffoldNetwork [100%] Linking CXX executable testScaffoldNetwork cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testScaffoldNetwork.dir/catch_main.cpp.o CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -o testScaffoldNetwork ../../../lib/libRDKitScaffoldNetwork.so.1.2020.09.4 ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [100%] Built target testScaffoldNetwork make[3]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' STATIC_LINK=0 RDKIT_LIBDIR=/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu//lib pg_buildext build /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit build-%v ### PostgreSQL 13 build ### make[2]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/build-13' gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fno-omit-frame-pointer -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o rdkit_io.o /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_io.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fno-omit-frame-pointer -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o mol_op.o /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function ‘mol_murckoscaffold’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:263:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 263 | CROMol scaffold = MolMurckoScaffold(mol); | ^~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function ‘mol_nm_hash’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:283:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 283 | char *str = computeNMMolHash(mol, opts); | ^~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:285:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 285 | char *res = pnstrdup(str, strlen(str)); | ^~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:278:7: warning: unused variable ‘len’ [-Wunused-variable] 278 | int len; | ^~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function ‘mol_adjust_query_properties’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:298:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 298 | char *data = PG_GETARG_CSTRING(1); | ^~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:304:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 304 | Mol *res = deconstructROMol(adj); | ^~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function ‘mol_to_svg’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:319:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 319 | char *legend = PG_GETARG_CSTRING(1); | ^~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function ‘fmcs_smiles’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:343:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 343 | char *res = pnstrdup(str, strlen(str)); | ^~~~ In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:34: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function ‘fmcs_mol2s_transition’: /usr/include/postgresql/13/server/fmgr.h:268:29: warning: initialization of ‘CROMol’ {aka ‘void *’} from ‘Datum’ {aka ‘long unsigned int’} makes pointer from integer without a cast [-Wint-conversion] 268 | #define PG_GETARG_DATUM(n) (fcinfo->args[n].value) | ^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:395:18: note: in expansion of macro ‘PG_GETARG_DATUM’ 395 | CROMol mol = PG_GETARG_DATUM(1); | ^~~~~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:411:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 411 | text *ts = (text *)palloc(ts_size); // new return value | ^~~~ In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:34: /usr/include/postgresql/13/server/fmgr.h:268:29: warning: initialization of ‘CROMol’ {aka ‘void *’} from ‘Datum’ {aka ‘long unsigned int’} makes pointer from integer without a cast [-Wint-conversion] 268 | #define PG_GETARG_DATUM(n) (fcinfo->args[n].value) | ^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:423:18: note: in expansion of macro ‘PG_GETARG_DATUM’ 423 | CROMol mol = PG_GETARG_DATUM(1); | ^~~~~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:431:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 431 | char *smiles = makeMolText(mol, &len, false, false); | ^~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function ‘fmcs_mols’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:469:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 469 | int32 ts_size = VARHDRSZ + strlen(str); | ^~~~~ In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:34: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function ‘fmcs_mol_transition’: /usr/include/postgresql/13/server/fmgr.h:268:29: warning: initialization of ‘CROMol’ {aka ‘void *’} from ‘Datum’ {aka ‘long unsigned int’} makes pointer from integer without a cast [-Wint-conversion] 268 | #define PG_GETARG_DATUM(n) (fcinfo->args[n].value) | ^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:491:18: note: in expansion of macro ‘PG_GETARG_DATUM’ 491 | CROMol mol = PG_GETARG_DATUM(1); | ^~~~~~~~~~~~~~~ In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:33: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:498:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 498 | PG_RETURN_INT32((int32)lst); | ^ /usr/include/postgresql/13/server/postgres.h:479:36: note: in definition of macro ‘Int32GetDatum’ 479 | #define Int32GetDatum(X) ((Datum) (X)) | ^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:498:5: note: in expansion of macro ‘PG_RETURN_INT32’ 498 | PG_RETURN_INT32((int32)lst); | ^~~~~~~~~~~~~~~ In file included from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:34: /usr/include/postgresql/13/server/fmgr.h:268:29: warning: initialization of ‘CROMol’ {aka ‘void *’} from ‘Datum’ {aka ‘long unsigned int’} makes pointer from integer without a cast [-Wint-conversion] 268 | #define PG_GETARG_DATUM(n) (fcinfo->args[n].value) | ^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:502:18: note: in expansion of macro ‘PG_GETARG_DATUM’ 502 | CROMol mol = PG_GETARG_DATUM(1); | ^~~~~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function ‘fmcs_smiles_transition’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:375:1: warning: control reaches end of non-void function [-Wreturn-type] 375 | } | ^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function ‘fmcs_mol_transition’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:510:1: warning: control reaches end of non-void function [-Wreturn-type] 510 | } | ^ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fno-omit-frame-pointer -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o bfp_op.o /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/bfp_op.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fno-omit-frame-pointer -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o sfp_op.o /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/sfp_op.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fno-omit-frame-pointer -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o rxn_op.o /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rxn_op.c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rxn_op.c:164:1: warning: multi-line comment [-Wcomment] 164 | // /* keep compiler quiet - no extra ; */ \ | ^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rxn_op.c: In function ‘reaction_to_svg’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rxn_op.c:179:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 179 | bool highlightByReactants = PG_GETARG_BOOL(1); | ^~~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fno-omit-frame-pointer -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o rdkit_gist.o /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c: In function ‘soergeldistsign’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:239:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 239 | uint8 *as = (uint8 *)VARDATA(a); | ^~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c: In function ‘soergeldist’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:274:16: warning: implicit declaration of function ‘floor’ [-Wimplicit-function-declaration] 274 | return (int) floor(10000*soergeldistsign(a, b)); | ^~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:274:16: warning: incompatible implicit declaration of built-in function ‘floor’ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:41:1: note: include ‘’ or provide a declaration of ‘floor’ 40 | #include "bitstring.h" +++ |+#include 41 | /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:261:10: warning: unused variable ‘d’ [-Wunused-variable] 261 | double d; | ^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c: In function ‘gmol_consistent’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:525:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 525 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:537:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 537 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:569:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 569 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c: In function ‘rdkit_consistent’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:657:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 657 | int siglen = SIGLEN(query); | ^~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:672:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 672 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c: In function ‘gsfp_consistent’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:707:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 707 | int sum, overlapSum, overlapN; | ^~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:713:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 713 | int nKey = (ISALLTRUE(key)) ? | ^~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c: In function ‘greaction_consistent’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:786:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 786 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:803:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 803 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:831:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 831 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ At top level: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:645:1: warning: ‘rdkit_consistent’ defined but not used [-Wunused-function] 645 | rdkit_consistent(GISTENTRY *entry, StrategyNumber strategy, bytea *key, bytea *query) | ^~~~~~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:260:1: warning: ‘soergeldist’ defined but not used [-Wunused-function] 260 | soergeldist(bytea *a, bytea *b) { | ^~~~~~~~~~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fno-omit-frame-pointer -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o bfp_gist.o /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/bfp_gist.c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/bfp_gist.c: In function ‘merge_key’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/bfp_gist.c:698:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 698 | int siglen = GBFP_INNER_SIGLEN(result); | ^~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fno-omit-frame-pointer -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o bfp_gin.o /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/bfp_gin.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fno-omit-frame-pointer -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o low_gist.o /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/low_gist.c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/low_gist.c: In function ‘gslfp_consistent’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/low_gist.c:409:30: warning: implicit declaration of function ‘searchSfpCache’ [-Wimplicit-function-declaration] 409 | fcinfo->flinfo->fn_extra = searchSfpCache( | ^~~~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/low_gist.c:409:28: warning: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 409 | fcinfo->flinfo->fn_extra = searchSfpCache( | ^ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fno-omit-frame-pointer -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o guc.o /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/guc.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fno-omit-frame-pointer -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o cache.o /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/cache.c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/cache.c: In function ‘createCache’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/cache.c:312:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 312 | methodsOrig = ctx->methods; | ^ g++ -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o adapter.o /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/adapter.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/smart_ptr.hpp:19, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Vector.h:23, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h:24, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Conformer.h:14, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RDKitBase.h:25, from /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/adapter.cpp:32: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fno-omit-frame-pointer -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o bitstring.o /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/bitstring.c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/bitstring.c: In function ‘bitstringUnion’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/bitstring.c:72:7: warning: unused variable ‘i’ [-Wunused-variable] 72 | int i; | ^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/bitstring.c: In function ‘bitstringIntersection’: /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/bitstring.c:106:7: warning: unused variable ‘i’ [-Wunused-variable] 106 | int i; | ^ g++ -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fno-omit-frame-pointer -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -shared -o rdkit.so rdkit_io.o mol_op.o bfp_op.o sfp_op.o rxn_op.o rdkit_gist.o bfp_gist.o bfp_gin.o low_gist.o guc.o cache.o adapter.o bitstring.o -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib/llvm-11/lib -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/rdkit-TKP8Bz/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -L/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu//lib -lRDKitMolDraw2D -lRDKitMolTransforms -lRDKitMolHash -lRDKitFMCS -lRDKitChemReactions -lRDKitChemTransforms -lRDKitFileParsers -lRDKitSmilesParse -lRDKitFingerprints -lRDKitSubgraphs -lRDKitDescriptors -lRDKitPartialCharges -lRDKitSubstructMatch -lRDKitGraphMol -lRDKitEigenSolvers -lRDKitDataStructs -lRDKitDepictor -lRDKitRDGeometryLib -lRDKitRDGeneral -pthread sed -e's/@RDKIT_PG_BFP_GIST_FETCH@/FUNCTION 9 gbfp_fetch (internal),/;' \ -e's/@RDKIT_GIN_BFP_TRICONSISTENT@/FUNCTION 6 gin_bfp_triconsistent(internal, int2, bfp, int4, internal, internal, internal),/' \ -e's/@RDKIT_PARALLEL_SAFE@/PARALLEL SAFE/' \ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit.sql.in > rdkit--3.8.sql /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o rdkit_io.bc /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_io.c /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o mol_op.bc /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:375:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:395:12: warning: incompatible integer to pointer conversion initializing 'CROMol' (aka 'void *') with an expression of type 'Datum' (aka 'unsigned long') [-Wint-conversion] CROMol mol = PG_GETARG_DATUM(1); ^ ~~~~~~~~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:423:12: warning: incompatible integer to pointer conversion initializing 'CROMol' (aka 'void *') with an expression of type 'Datum' (aka 'unsigned long') [-Wint-conversion] CROMol mol = PG_GETARG_DATUM(1); ^ ~~~~~~~~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:491:12: warning: incompatible integer to pointer conversion initializing 'CROMol' (aka 'void *') with an expression of type 'Datum' (aka 'unsigned long') [-Wint-conversion] CROMol mol = PG_GETARG_DATUM(1); ^ ~~~~~~~~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:498:21: warning: cast to smaller integer type 'int32' (aka 'int') from 'void *' [-Wvoid-pointer-to-int-cast] PG_RETURN_INT32((int32)lst); ^~~~~~~~~~ /usr/include/postgresql/13/server/fmgr.h:353:50: note: expanded from macro 'PG_RETURN_INT32' #define PG_RETURN_INT32(x) return Int32GetDatum(x) ^ /usr/include/postgresql/13/server/postgres.h:479:36: note: expanded from macro 'Int32GetDatum' #define Int32GetDatum(X) ((Datum) (X)) ^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:502:12: warning: incompatible integer to pointer conversion initializing 'CROMol' (aka 'void *') with an expression of type 'Datum' (aka 'unsigned long') [-Wint-conversion] CROMol mol = PG_GETARG_DATUM(1); ^ ~~~~~~~~~~~~~~~~~~ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:510:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 7 warnings generated. /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o bfp_op.bc /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/bfp_op.c /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o sfp_op.bc /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/sfp_op.c /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o rxn_op.bc /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rxn_op.c /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o rdkit_gist.bc /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o bfp_gist.bc /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/bfp_gist.c /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o bfp_gin.bc /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/bfp_gin.c /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o low_gist.bc /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/low_gist.c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/low_gist.c:409:30: warning: implicit declaration of function 'searchSfpCache' is invalid in C99 [-Wimplicit-function-declaration] fcinfo->flinfo->fn_extra = searchSfpCache( ^ /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/low_gist.c:409:28: warning: incompatible integer to pointer conversion assigning to 'void *' from 'int' [-Wint-conversion] fcinfo->flinfo->fn_extra = searchSfpCache( ^ ~~~~~~~~~~~~~~~ 2 warnings generated. /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o guc.bc /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/guc.c /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o cache.bc /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/cache.c /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/cache.c:312:17: warning: assigning to 'MemoryContextMethods *' (aka 'struct MemoryContextMethods *') from 'const MemoryContextMethods *' (aka 'const struct MemoryContextMethods *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] methodsOrig = ctx->methods; ^ ~~~~~~~~~~~~ 1 warning generated. /usr/bin/clang-11 -xc++ -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -emit-llvm -c -o adapter.bc /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/adapter.cpp /usr/lib/llvm-11/bin/opt -module-summary -f adapter.bc -o adapter.bc /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o bitstring.bc /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/bitstring.c make[2]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/build-13' ### End 13 build ### (cd /build/rdkit-TKP8Bz/rdkit-202009.4/Code; doxygen doxygen/doxygen.config) warning: Tag 'TCL_SUBST' at line 213 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'SYMBOL_CACHE_SIZE' at line 337 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'SHOW_DIRECTORIES' at line 557 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'COLS_IN_ALPHA_INDEX' at line 869 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'HTML_ALIGN_MEMBERS' at line 971 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'USE_INLINE_TREES' at line 1162 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'XML_SCHEMA' at line 1425 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'XML_DTD' at line 1431 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'PERL_PATH' at line 1596 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 1617 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: argument 'a4wide' for option PAPER_TYPE is not a valid enum value Using the default: a4! warning: doxygen no longer ships with the FreeSans font. You may want to clear or change DOT_FONTNAME. Otherwise you run the risk that the wrong font is being used for dot generated graphs. Doxygen version used: 1.9.1 Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching INPUT for files to process... 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/build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/TautomerQuery Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Trajectory Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Catalogs Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/Cluster Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/Cluster/Murtagh Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/Data Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/InfoTheory Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataManip Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataManip/MetricMatrixCalc Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/hash Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/hash/detail Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Alignment Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/EigenSolvers Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Optimizer Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Features Searching for files in directory /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ChemicalFeatures Reading and parsing tag files Parsing files Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Abbreviations/Abbreviations.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Abbreviations/Abbreviations.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Atom.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Atom.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/atomic_data.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/atomic_data.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/AtomIterators.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/AtomIterators.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Bond.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Bond.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/BondIterators.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/BondIterators.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Canon.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Canon.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/CartesianProduct.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/CartesianProduct.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/Enumerate.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/Enumerate.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerateBase.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerateBase.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/RandomSample.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/RandomSample.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/PreprocessRxn.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/PreprocessRxn.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Reaction.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Reaction.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionFingerprints.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionFingerprints.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionParser.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionParser.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionPickler.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionPickler.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionRunner.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionRunner.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionUtils.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionUtils.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/SanitizeRxn.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/SanitizeRxn.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemTransforms/ChemTransforms.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemTransforms/ChemTransforms.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemTransforms/MolFragmenter.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemTransforms/MolFragmenter.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Chirality.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Chirality.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/CIPLabeler.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/CIPLabeler.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/CIPMol.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/CIPMol.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Configuration.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Configuration.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Sp2Bond.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Sp2Bond.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Descriptor.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Descriptor.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Digraph.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Digraph.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Edge.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Edge.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Mancude.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Mancude.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Node.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Node.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Priority.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Priority.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Pairlist.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Pairlist.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule1a.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule1a.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule1b.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule1b.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule2.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule2.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule3.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule3.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4a.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4a.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4b.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4b.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4c.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4c.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5New.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5New.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule6.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule6.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rules.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rules.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/SequenceRule.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/SequenceRule.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Sort.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Sort.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/TooManyNodesException.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/TooManyNodesException.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Conformer.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Conformer.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor/DepictUtils.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor/DepictUtils.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor/EmbeddedFrag.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor/EmbeddedFrag.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor/RDDepictor.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor/RDDepictor.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Deprotect/Deprotect.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Deprotect/Deprotect.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/AtomFeat.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/AtomFeat.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/AUTOCORR2D.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/AUTOCORR2D.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/AUTOCORR3D.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/AUTOCORR3D.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/BCUT.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/BCUT.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/ConnectivityDescriptors.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/ConnectivityDescriptors.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/CoulombMat.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/CoulombMat.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/Crippen.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/Crippen.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/Data3Ddescriptors.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/Data3Ddescriptors.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/EEM.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/EEM.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/GETAWAY.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/GETAWAY.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/Lipinski.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/Lipinski.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/MolDescriptors.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/MolDescriptors.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/MolDescriptors3D.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/MolDescriptors3D.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/MolSurf.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/MolSurf.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/MORSE.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/MORSE.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/MQN.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/MQN.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/PBF.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/PBF.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/PMI.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/PMI.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/Property.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/Property.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/RDF.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/RDF.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/RegisterDescriptor.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/RegisterDescriptor.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/USRDescriptor.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/USRDescriptor.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/WHIM.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/WHIM.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/details.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/details.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/Embedder.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/Embedder.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/FileParsers.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/FileParsers.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/FileParserUtils.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/FileParserUtils.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/GeneralFileReader.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/GeneralFileReader.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolFileStereochem.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolFileStereochem.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupParsing.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupParsing.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolSupplier.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolSupplier.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolWriters.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MolWriters.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/PNGParser.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/PNGParser.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/ProximityBonds.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/ProximityBonds.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/SequenceParsers.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/SequenceParsers.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/SequenceWriters.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/SequenceWriters.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterCatalog.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterCatalog.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/Filters.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/Filters.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/AtomPairGenerator.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/AtomPairGenerator.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/AtomPairs.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/AtomPairs.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/FingerprintGenerator.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/FingerprintGenerator.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/Fingerprints.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/Fingerprints.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/FingerprintUtil.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/FingerprintUtil.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MACCS.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MACCS.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MHFP.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MHFP.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganFingerprints.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganFingerprints.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/RDKitFPGenerator.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/RDKitFPGenerator.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/Composition2N.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/Composition2N.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/DebugTrace.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/DebugTrace.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/FMCS.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/FMCS.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/Graph.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/Graph.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/MatchTable.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/MatchTable.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/RingMatchTableSet.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/RingMatchTableSet.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/Seed.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/Seed.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/SeedSet.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/SeedSet.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/SubstructMatchCustom.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/SubstructMatchCustom.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/SubstructureCache.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/SubstructureCache.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/Target.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/Target.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/TargetMatch.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/TargetMatch.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/FFConvenience.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/FFConvenience.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatGenerator.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatGenerator.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatParams.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatParams.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/FragFPGenerator.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/FragFPGenerator.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/GraphMol.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/GraphMol.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MMPA/MMPA.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MMPA/MMPA.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign/AlignMolecules.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign/AlignMolecules.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolBundle.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolBundle.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolCatalog/MolCatalog.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolCatalog/MolCatalog.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolCatalog/MolCatalogParams.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolCatalog/MolCatalogParams.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawText.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawText.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextCairo.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextCairo.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFT.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFT.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTCairo.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTCairo.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTJS.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTJS.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTQt.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTQt.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTSVG.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTSVG.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextJS.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextJS.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextQt.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextQt.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextSVG.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextSVG.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DJS.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DJS.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DQt.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DQt.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MultiMolDraw2D.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MultiMolDraw2D.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolHash/mf.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolHash/mf.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolHash/MolHash.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolHash/MolHash.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolHash/nmmolhash.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolHash/nmmolhash.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolInterchange/details.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolInterchange/details.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolInterchange/MolInterchange.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolInterchange/MolInterchange.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolOps.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolOps.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolPickler.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolPickler.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Charge.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Charge.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Fragment.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Fragment.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Metal.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Metal.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/MolStandardize.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/MolStandardize.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Normalize.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Normalize.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Tautomer.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Tautomer.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Validate.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Validate.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolTransforms/MolTransforms.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolTransforms/MolTransforms.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MonomerInfo.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MonomerInfo.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/new_canon.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/new_canon.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/PartialCharges/GasteigerCharges.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/PartialCharges/GasteigerCharges.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/PartialCharges/GasteigerParams.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/PartialCharges/GasteigerParams.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/PeriodicTable.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/PeriodicTable.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/QueryAtom.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/QueryAtom.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/QueryBond.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/QueryBond.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/QueryOps.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/QueryOps.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RDKitBase.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RDKitBase.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RDKitQueries.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RDKitQueries.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ReducedGraphs/ReducedGraphs.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ReducedGraphs/ReducedGraphs.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Resonance.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Resonance.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupCore.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupCore.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupData.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupData.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupMatch.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupMatch.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupScore.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupScore.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupUtils.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupUtils.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RingInfo.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RingInfo.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Rings.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Rings.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ROMol.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ROMol.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RWMol.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RWMol.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SanitException.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SanitException.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/detail.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/detail.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SLNParse/SLNAttribs.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SLNParse/SLNAttribs.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SLNParse/SLNParse.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SLNParse/SLNParse.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SLNParse/SLNParseOps.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SLNParse/SLNParseOps.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/primes.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/primes.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/SmartsWrite.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/SmartsWrite.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesParse.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesParse.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesParseOps.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesParseOps.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesWrite.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesWrite.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/StereoGroup.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/StereoGroup.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/StructChecker/Pattern.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/StructChecker/Pattern.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/StructChecker/ReCharge.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/StructChecker/ReCharge.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/StructChecker/Stereo.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/StructChecker/Stereo.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/StructChecker/StripSmallFragments.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/StructChecker/StripSmallFragments.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/StructChecker/StructChecker.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/StructChecker/StructChecker.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/StructChecker/StructCheckerOptions.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/StructChecker/StructCheckerOptions.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/StructChecker/Tautomer.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/StructChecker/Tautomer.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/StructChecker/Utilites.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/StructChecker/Utilites.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Subgraphs/Subgraphs.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Subgraphs/Subgraphs.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Subgraphs/SubgraphUtils.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Subgraphs/SubgraphUtils.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstanceGroup.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstanceGroup.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Substruct/SubstructMatch.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Substruct/SubstructMatch.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Substruct/SubstructUtils.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Substruct/SubstructUtils.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary/PatternFactory.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary/PatternFactory.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/TautomerQuery/TautomerQuery.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/TautomerQuery/TautomerQuery.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Trajectory/Snapshot.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Trajectory/Snapshot.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Trajectory/Trajectory.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Trajectory/Trajectory.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Catalogs/Catalog.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Catalogs/Catalog.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Catalogs/CatalogEntry.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Catalogs/CatalogEntry.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Catalogs/CatalogParams.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Catalogs/CatalogParams.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/base64.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/base64.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/BitOps.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/BitOps.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/BitVect.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/BitVect.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/BitVects.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/BitVects.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/BitVectUtils.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/BitVectUtils.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/DatastructsException.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/DatastructsException.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/DatastructsStreamOps.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/DatastructsStreamOps.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/DiscreteDistMat.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/DiscreteDistMat.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/DiscreteValueVect.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/DiscreteValueVect.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/ExplicitBitVect.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/ExplicitBitVect.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/FPBReader.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/FPBReader.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/MultiFPBReader.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/MultiFPBReader.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/SparseBitVect.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/SparseBitVect.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/SparseIntVect.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/SparseIntVect.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/AndQuery.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/AndQuery.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/EqualityQuery.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/EqualityQuery.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/GreaterEqualQuery.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/GreaterEqualQuery.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/GreaterQuery.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/GreaterQuery.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/LessEqualQuery.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/LessEqualQuery.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/LessQuery.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/LessQuery.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/NullQueryAlgebra.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/NullQueryAlgebra.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/OrQuery.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/OrQuery.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/Query.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/Query.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/QueryObjects.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/QueryObjects.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/RangeQuery.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/RangeQuery.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/SetQuery.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/SetQuery.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/XOrQuery.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query/XOrQuery.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/InfoTheory/CorrMatGenerator.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/InfoTheory/CorrMatGenerator.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/InfoTheory/InfoBitRanker.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/InfoTheory/InfoBitRanker.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/InfoTheory/InfoGainFuncs.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/InfoTheory/InfoGainFuncs.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/MetricFuncs.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/MetricFuncs.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/DistPicker.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/DistPicker.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/HierarchicalClusterPicker.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/HierarchicalClusterPicker.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/LeaderPicker.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/LeaderPicker.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/MaxMinPicker.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/MaxMinPicker.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/BadFileException.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/BadFileException.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/BoostEndInclude.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/BoostEndInclude.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/BoostStartInclude.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/BoostStartInclude.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/ConcurrentQueue.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/ConcurrentQueue.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/Dict.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/Dict.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/Exceptions.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/Exceptions.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/export.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/export.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/FileParseException.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/FileParseException.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/hanoiSort.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/hanoiSort.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/Invariant.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/Invariant.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/LocaleSwitcher.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/LocaleSwitcher.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/Ranking.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/Ranking.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/RDAny.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/RDAny.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/RDConfig.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/RDConfig.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/RDLog.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/RDLog.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/RDProps.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/RDProps.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/RDThreads.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/RDThreads.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/RDValue-doublemagic.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/RDValue-doublemagic.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/RDValue-taggedunion.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/RDValue-taggedunion.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/RDValue.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/RDValue.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/StreamOps.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/StreamOps.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/types.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/types.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/utils.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/utils.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/versions.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral/versions.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/boost_numpy.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/boost_numpy.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/import_array.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/import_array.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/pyint_api.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/pyint_api.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/PySequenceHolder.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/PySequenceHolder.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost/python_streambuf.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/BoundsMatrix.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/BoundsMatrix.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/ChiralSet.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/ChiralSet.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/ChiralViolationContrib.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/ChiralViolationContrib.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/DistGeomUtils.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/DistGeomUtils.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/DistViolationContrib.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/DistViolationContrib.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/FourthDimContrib.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/FourthDimContrib.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/TriangleSmooth.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/TriangleSmooth.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/Contrib.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/Contrib.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/ForceField.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/ForceField.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/AngleBend.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/AngleBend.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/AngleConstraint.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/AngleConstraint.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/BondStretch.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/BondStretch.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/Contribs.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/Contribs.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/DistanceConstraint.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/DistanceConstraint.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/Nonbonded.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/Nonbonded.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/OopBend.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/OopBend.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/Params.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/Params.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/PositionConstraint.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/PositionConstraint.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/StretchBend.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/StretchBend.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/TorsionAngle.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/TorsionAngle.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/TorsionConstraint.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/TorsionConstraint.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/AngleBend.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/AngleBend.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/AngleConstraint.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/AngleConstraint.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/BondStretch.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/BondStretch.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/Contribs.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/Contribs.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/DistanceConstraint.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/DistanceConstraint.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/Inversion.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/Inversion.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/Nonbonded.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/Nonbonded.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/Params.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/Params.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/PositionConstraint.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/PositionConstraint.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/TorsionAngle.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/TorsionAngle.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/TorsionConstraint.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/TorsionConstraint.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Alignment/AlignPoints.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Alignment/AlignPoints.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Conrec.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Conrec.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Matrix.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Matrix.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Optimizer/BFGSOpt.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Optimizer/BFGSOpt.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/SquareMatrix.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/SquareMatrix.h... P/build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h:61: warning: documented symbol 'for experimental torsion angle RDKit::DGeomHelpers::preferences' was not declared or defined. /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolHash/nmmolhash.h:25: warning: documented symbol 'enum RDKIT_MOLHASH_EXPORT RDKit::MolHash::HashFunction' was not declared or defined. /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolHash/nmmolhash.h:47: warning: documented symbol 'enum RDKIT_MOLHASH_EXPORT RDKit::MolHash::StripType' was not declared or defined. /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h:68: warning: documented symbol 'enum RDKIT_SCAFFOLDNETWORK_EXPORT RDKit::ScaffoldNetwork::EdgeType' was not declared or defined. /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:133: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:70: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:123: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:130: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/QueryOps.h:515: warning: Found unknown command '\overloadquery' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/QueryOps.h:524: warning: Found unknown command '\overloadquery' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:73: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:126: warning: Found unknown command '\override' reprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/SymmMatrix.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/SymmMatrix.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Vector.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Vector.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Grid3D.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Grid3D.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/GridUtils.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/GridUtils.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/point.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Transform.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Transform.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Transform2D.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Transform2D.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Transform3D.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Transform3D.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/UniformGrid3D.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/UniformGrid3D.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Utils.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Utils.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Features/Feature.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Features/Feature.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ChemicalFeatures/ChemicalFeature.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ChemicalFeatures/ChemicalFeature.h... Preprocessing /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ChemicalFeatures/FreeChemicalFeature.h... Parsing file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ChemicalFeatures/FreeChemicalFeature.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Computing nesting relations for classes... Associating documentation with classes... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file Abbreviations.h... Generating code for file AcidBaseCatalogEntry.h... Generating code for file AcidBaseCatalogParams.h... Generating code for file AcidBaseCatalogUtils.h... Generating code for file AlignMolecules.h... Generating code for file AlignPoints.h... Generating code for file AndQuery.h... Generating code for file AngleBend.h... Generating code for file AngleBend.h... Generating code for file AngleConstraint.h... Generating code for file AngleConstraint.h... Generating code for file Atom.h... Generating code for file AtomFeat.h... Generating code for file atomic_data.h... Generating code for file AtomIterators.h... Generating code for file AtomPairGenerator.h... Generating code for file AtomPairs.h... Generating code for file AtomTyper.h... Generating code for file AtomTyper.h... Generating code for file AUTOCORR2D.h... Generating code for file AUTOCORR3D.h... Generating code for file BadFileException.h... Generating code for file base64.h... Generating code for file BCUT.h... Generating code for file BFGSOpt.h... Generating code for file BitOps.h... Generating code for file BitVect.h... Generating code for file BitVects.h... Generating code for file BitVectUtils.h... Generating code for file Bond.h... Generating code for file BondIterators.h... Generating code for file BondStretch.h... Generating code for file BondStretch.h... Generating code for file boost_numpy.h... Generating code for file BoostEndInclude.h... Generating code for file BoostStartInclude.h... Generating code for file BoundsMatrix.h... Generating code for file BoundsMatrixBuilder.h... Generating code for file Builder.h... Generating code for file Builder.h... Generating code for file Canon.h... Generating code for file CartesianProduct.h... Generating code for file Catalog.h... Generating code for file CatalogEntry.h... Generating code for file CatalogParams.h... Generating code for file Charge.h... Generating code for file ChemicalFeature.h... Generating code for file ChemTransforms.h... Generating code for file Chirality.h... Generating code for file ChiralSet.h... Generating code for file ChiralViolationContrib.h... Generating code for file CIPLabeler.h... Generating code for file CIPMol.h... Generating code for file Composition2N.h... Generating code for file ConcurrentQueue.h... Generating code for file Configuration.h... Generating code for file Conformer.h... Generating code for file ConnectivityDescriptors.h... Generating code for file Conrec.h... Generating code for file Contrib.h... Generating code for file Contribs.h... Generating code for file Contribs.h... Generating code for file CorrMatGenerator.h... Generating code for file CoulombMat.h... Generating code for file Crippen.h... Generating code for file Data3Ddescriptors.h... Generating code for file DatastructsException.h... Generating code for file DatastructsStreamOps.h... Generating code for file DebugTrace.h... Generating code for file DepictUtils.h... Generating code for file Deprotect.h... Generating code for file Descriptor.h... Generating code for file detail.h... Generating code for file details.h... Generating code for file details.h... Generating code for file Dict.h... Generating code for file Digraph.h... Generating code for file DiscreteDistMat.h... Generating code for file DiscreteValueVect.h... Generating code for file DistanceConstraint.h... Generating code for file DistanceConstraint.h... Generating code for file DistGeomUtils.h... Generating code for file DistPicker.h... Generating code for file DistViolationContrib.h... Generating code for file DrawText.h... Generating code for file DrawTextCairo.h... Generating code for file DrawTextFT.h... Generating code for file DrawTextFTCairo.h... Generating code for file DrawTextFTJS.h... Generating code for file DrawTextFTQt.h... Generating code for file DrawTextFTSVG.h... Generating code for file DrawTextJS.h... Generating code for file DrawTextQt.h... Generating code for file DrawTextSVG.h... Generating code for file DuplicatedSeedCache.h... Generating code for file Edge.h... Generating code for file EEM.h... Generating code for file EmbeddedFrag.h... Generating code for file Embedder.h... Generating code for file Enumerate.h... Generating code for file EnumerateBase.h... Generating code for file EnumerateTypes.h... Generating code for file EnumerationPickler.h... Generating code for file EnumerationStrategyBase.h... Generating code for file EqualityQuery.h... Generating code for file EvenSamplePairs.h... Generating code for file Exceptions.h... Generating code for file ExplicitBitVect.h... Generating code for file export.h... Generating code for file Feature.h... Generating code for file FeatureParser.h... Generating code for file FFConvenience.h... Generating code for file FileParseException.h... Generating code for file FileParsers.h... Generating code for file FileParserUtils.h... Generating code for file FilterCatalog.h... Generating code for file FilterCatalogEntry.h... Generating code for file FilterMatcherBase.h... Generating code for file FilterMatchers.h... Generating code for file Filters.h... Generating code for file FingerprintGenerator.h... Generating code for file Fingerprints.h... Generating code for file FingerprintUtil.h... Generating code for file FMCS.h... Generating code for file ForceField.h... Generating code for file FourthDimContrib.h... Generating code for file FPBReader.h... Generating code for file FragCatalogEntry.h... Generating code for file FragCatalogUtils.h... Generating code for file FragCatGenerator.h... Generating code for file FragCatParams.h... Generating code for file FragFPGenerator.h... Generating code for file Fragment.h... Generating code for file FragmentCatalogEntry.h... Generating code for file FragmentCatalogParams.h... Generating code for file FragmentCatalogUtils.h... Generating code for file FreeChemicalFeature.h... Generating code for file FunctionalGroupHierarchy.h... Generating code for file GasteigerCharges.h... Generating code for file GasteigerParams.h... Generating code for file GeneralFileReader.h... Generating code for file GETAWAY.h... Generating code for file Graph.h... Generating code for file GraphMol.h... Generating code for file GreaterEqualQuery.h... Generating code for file GreaterQuery.h... Generating code for file Grid3D.h... Generating code for file GridUtils.h... Generating code for file hanoiSort.h... Generating code for file HierarchicalClusterPicker.h... Generating code for file import_array.h... Generating code for file InfoBitRanker.h... Generating code for file InfoGainFuncs.h... Generating code for file Invariant.h... Generating code for file Inversion.h... Generating code for file LeaderPicker.h... Generating code for file LessEqualQuery.h... Generating code for file LessQuery.h... Generating code for file Lipinski.h... Generating code for file LocaleSwitcher.h... Generating code for file MACCS.h... Generating code for file Mancude.h... Generating code for file MatchTable.h... Generating code for file Matrix.h... Generating code for file MaximumCommonSubgraph.h... Generating code for file MaxMinPicker.h... Generating code for file Metal.h... Generating code for file MetricFuncs.h... Generating code for file MetricMatrixCalc.h... Generating code for file mf.h... Generating code for file MHFP.h... Generating code for file MMFF.h... Generating code for file MMPA.h... Generating code for file MolBundle.h... Generating code for file MolCatalog.h... Generating code for file MolCatalogEntry.h... Generating code for file MolCatalogParams.h... Generating code for file MolChemicalFeature.h... Generating code for file MolChemicalFeatureDef.h... Generating code for file MolChemicalFeatureFactory.h... Generating code for file MolData3Ddescriptors.h... Generating code for file MolDescriptors.h... Generating code for file MolDescriptors3D.h... Generating code for file MolDraw2D.h... Generating code for file MolDraw2DCairo.h... Generating code for file MolDraw2DDetails.h... Generating code for file MolDraw2DJS.h... Generating code for file MolDraw2DQt.h... Generating code for file MolDraw2DSVG.h... Generating code for file MolDraw2DUtils.h... Generating code for file MolDraw2Dwx.h... Generating code for file MolEnumerator.h... Generating code for file MolFileStereochem.h... Generating code for file MolFragmenter.h... Generating code for file MolHash.h... Generating code for file MolInterchange.h... Generating code for file MolOps.h... Generating code for file MolPickler.h... Generating code for file MolSGroupParsing.h... Generating code for file MolSGroupWriting.h... Generating code for file MolStandardize.h... Generating code for file MolSupplier.h... Generating code for file MolSurf.h... Generating code for file MolTransforms.h... Generating code for file MolWriters.h... Generating code for file MonomerInfo.h... Generating code for file MorganFingerprints.h... Generating code for file MorganGenerator.h... Generating code for file MORSE.h... Generating code for file MQN.h... Generating code for file MultiFPBReader.h... Generating code for file MultiMolDraw2D.h... Generating code for file MultithreadedMolSupplier.h... Generating code for file MultithreadedSDMolSupplier.h... Generating code for file MultithreadedSmilesMolSupplier.h... Generating code for file new_canon.h... Generating code for file nmmolhash.h... Generating code for file Node.h... Generating code for file Nonbonded.h... Generating code for file Nonbonded.h... Generating code for file Normalize.h... Generating code for file NullQueryAlgebra.h... Generating code for file O3AAlignMolecules.h... Generating code for file OopBend.h... Generating code for file OrQuery.h... Generating code for file Pairlist.h... Generating code for file Params.h... Generating code for file Params.h... Generating code for file Pattern.h... Generating code for file PatternFactory.h... Generating code for file PBF.h... Generating code for file PeriodicTable.h... Generating code for file PMI.h... Generating code for file PNGParser.h... Generating code for file point.h... Generating code for file PositionConstraint.h... Generating code for file PositionConstraint.h... Generating code for file PowerEigenSolver.h... Generating code for file PreprocessRxn.h... Generating code for file primes.h... Generating code for file Priority.h... Generating code for file Property.h... Generating code for file ProximityBonds.h... Generating code for file pyint_api.h... Generating code for file PySequenceHolder.h... Generating code for file python.h... Generating code for file python_streambuf.h... Generating code for file Query.h... Generating code for file QueryAtom.h... Generating code for file QueryBond.h... Generating code for file QueryObjects.h... Generating code for file QueryOps.h... Generating code for file RandomSample.h... Generating code for file RandomSampleAllBBs.h... Generating code for file RangeQuery.h... Generating code for file Ranking.h... Generating code for file RDAny.h... Generating code for file RDConfig.h... Generating code for file RDDepictor.h... Generating code for file RDF.h... Generating code for file RDKitBase.h... Generating code for file RDKitFPGenerator.h... Generating code for file RDKitQueries.h... Generating code for file RDLog.h... Generating code for file RDProps.h... Generating code for file RDThreads.h... Generating code for file RDValue-doublemagic.h... Generating code for file RDValue-taggedunion.h... Generating code for file RDValue.h... Generating code for file Reaction.h... Generating code for file ReactionFingerprints.h... Generating code for file ReactionParser.h... Generating code for file ReactionPickler.h... Generating code for file ReactionRunner.h... Generating code for file ReactionUtils.h... Generating code for file ReCharge.h... Generating code for file ReducedGraphs.h... Generating code for file RegisterDescriptor.h... Generating code for file Resonance.h... Generating code for file RGroupCore.h... Generating code for file RGroupData.h... Generating code for file RGroupDecomp.h... Generating code for file RGroupDecompData.h... Generating code for file RGroupMatch.h... Generating code for file RGroupScore.h... Generating code for file RGroupUtils.h... Generating code for file RingInfo.h... Generating code for file RingMatchTableSet.h... Generating code for file Rings.h... Generating code for file ROMol.h... Generating code for file Rule1a.h... Generating code for file Rule1b.h... Generating code for file Rule2.h... Generating code for file Rule3.h... Generating code for file Rule4a.h... Generating code for file Rule4b.h... Generating code for file Rule4c.h... Generating code for file Rule5.h... Generating code for file Rule5New.h... Generating code for file Rule6.h... Generating code for file Rules.h... Generating code for file RWMol.h... Generating code for file SanitException.h... Generating code for file SanitizeRxn.h... Generating code for file ScaffoldNetwork.h... Generating code for file Seed.h... Generating code for file SeedSet.h... Generating code for file SequenceParsers.h... Generating code for file SequenceRule.h... Generating code for file SequenceWriters.h... Generating code for file SetQuery.h... Generating code for file ShapeEncoder.h... Generating code for file ShapeUtils.h... Generating code for file SLNAttribs.h... Generating code for file SLNParse.h... Generating code for file SLNParseOps.h... Generating code for file SmartsWrite.h... Generating code for file SmilesParse.h... Generating code for file SmilesParseOps.h... Generating code for file SmilesWrite.h... Generating code for file Snapshot.h... Generating code for file Sort.h... Generating code for file Sp2Bond.h... Generating code for file SparseBitVect.h... Generating code for file SparseIntVect.h... Generating code for file SquareMatrix.h... Generating code for file Stereo.h... Generating code for file StereoGroup.h... Generating code for file StreamOps.h... Generating code for file StretchBend.h... Generating code for file StripSmallFragments.h... Generating code for file StructChecker.h... Generating code for file StructCheckerOptions.h... Generating code for file Subgraphs.h... Generating code for file SubgraphUtils.h... Generating code for file SubstanceGroup.h... Generating code for file SubstructLibrary.h... Generating code for file SubstructLibrarySerialization.h... Generating code for file SubstructMatch.h... Generating code for file SubstructMatchCustom.h... Generating code for file SubstructureCache.h... Generating code for file SubstructUtils.h... Generating code for file SymmMatrix.h... Generating code for file Target.h... Generating code for file TargetMatch.h... Generating code for file Tautomer.h... Generating code for file Tautomer.h... Generating code for file TautomerCatalogEntry.h... Generating code for file TautomerCatalogParams.h... Generating code for file TautomerCatalogUtils.h... Generating code for file TautomerQuery.h... Generating code for file Tetrahedral.h... Generating code for file TooManyNodesException.h... Generating code for file TopologicalTorsionGenerator.h... Generating code for file TorsionAngle.h... Generating code for file TorsionAngle.h... Generating code for file TorsionAngleM6.h... Generating code for file TorsionConstraint.h... Generating code for file TorsionConstraint.h... Generating code for file TorsionPreferences.h... Generating code for file Trajectory.h... Generating code for file Transform.h... Generating code for file Transform2D.h... Generating code for file Transform3D.h... Generating code for file TransformCatalogEntry.h... Generating code for file TransformCatalogParams.h... Generating code for file TransformCatalogUtils.h... Generating code for file TriangleSmooth.h... Generating code for file types.h... Generating code for file UFF.h... Generating code for file UniformGrid3D.h... Generating code for file USRDescriptor.h... Generating code for file Utilites.h... Generating code for file Utils.h... Generating code for file utils.h... Generating code for file Validate.h... Generating code for file Vector.h... Generating code for file versions.h... Generating code for file WHIM.h... Generating code for file XOrQuery.h... Generating file documentation... Generating docs for file Abbreviations.h... Generating docs for file AcidBaseCatalogEntry.h... Generating docs for file AcidBaseCatalogParams.h... Generating docs for file AcidBaseCatalogUtils.h... Generating docs for file AlignMolecules.h... Generating docs for file AlignPoints.h... Generating docs for file AndQuery.h... Generat/build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/BitOps.h:184: warning: found at different nesting level (7) than expected (4) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/BitOps.h:185: warning: end of comment block while expecting command ing docs for file AngleBend.h... Generating docs for file AngleBend.h... Generating docs for file AngleConstraint.h... Generating docs for file AngleConstraint.h... Generating docs for file Atom.h... Generating docs for file AtomFeat.h... Generating docs for file atomic_data.h... Generating docs for file AtomIterators.h... Generating docs for file AtomPairGenerator.h... Generating docs for file AtomPairs.h... Generating docs for file AtomTyper.h... Generating docs for file AtomTyper.h... Generating docs for file AUTOCORR2D.h... Generating docs for file AUTOCORR3D.h... Generating docs for file BadFileException.h... Generating docs for file base64.h... Generating docs for file BCUT.h... Generating docs for file BFGSOpt.h... Generating docs for file BitOps.h... Generating docs for file BitVect.h... Generating docs for file BitVects.h... Generating docs for file BitVectUtils.h... Generating docs for file Bond.h... Generating docs for file BondIterators.h... Generating docs for file BondStretch.h... Generating docs for file BondStretch.h... Generating docs for file boost_numpy.h... Generating docs for file BoostEndInclude.h... Generating docs for file BoostStartInclude.h... Generating docs for file BoundsMatrix.h... Generating docs for file BoundsMatrixBuilder.h... Generating docs for file Builder.h... Generating docs for file Builder.h... Generating docs for file Canon.h... Generating docs for file CartesianProduct.h... Generating docs for file Catalog.h... Generating docs for file CatalogEntry.h... Generating docs for file CatalogParams.h... Generating docs for file Charge.h... Generating docs for file ChemicalFeature.h... Generating docs for file ChemTransforms.h... 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Generating docs for file MACCS.h... Generating docs for file Mancude.h... Generating docs for file MatchTable.h... Generating docs for file Matrix.h... Generating docs for file MaximumCommonSubgraph.h... Generating docs for file MaxMinPicker.h... Generating docs for file Metal.h... Generating docs for file MetricFuncs.h... Generating docs for file MetricMatrixCalc.h... Generating docs for file mf.h... Generating docs for file MHFP.h... Generating docs for file MMFF.h... Generating docs for file MMPA.h... Generating docs for file MolBundle.h... Generating docs for file MolCatalog.h... Generating docs for file MolCatalogEntry.h... Generating docs for file MolCatalogParams.h... Generating docs for file MolChemicalFeature.h... Generating docs for file MolChemicalFeatureDef.h... Generating docs for file MolChemicalFeatureFactory.h... Generating docs for file MolData3Ddescriptors.h... Generating docs for file MolDescriptors.h... Generating docs for file MolDescriptors3D.h... Generating docs for file MolDraw2D.h... Generating docs for file MolDraw2DCairo.h... Generating docs for file MolDraw2DDetails.h... Generating docs for file MolDraw2DJS.h... Generating docs for file MolDraw2DQt.h... Generating docs for file MolDraw2DSVG.h... Generating docs for file MolDraw2DUtils.h... Generating docs for file MolDraw2Dwx.h... Generating docs for file MolEnumerator.h... Generating docs for file MolFileStereochem.h... Generating docs for file MolFragmenter.h... Generating docs for file MolHash.h... Generating docs for file MolInterchange.h... Generating docs for file MolOps.h... Generating docs for file MolPickler./build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/QueryOps.h:515: warning: Found unknown command '\overloadquery' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/QueryOps.h:524: warning: Found unknown command '\overloadquery' h... Generating docs for file MolSGroupParsing.h... Generating docs for file MolSGroupWriting.h... Generating docs for file MolStandardize.h... Generating docs for file MolSupplier.h... Generating docs for file MolSurf.h... Generating docs for file MolTransforms.h... Generating docs for file MolWriters.h... Generating docs for file MonomerInfo.h... Generating docs for file MorganFingerprints.h... Generating docs for file MorganGenerator.h... Generating docs for file MORSE.h... Generating docs for file MQN.h... Generating docs for file MultiFPBReader.h... Generating docs for file MultiMolDraw2D.h... Generating docs for file MultithreadedMolSupplier.h... Generating docs for file MultithreadedSDMolSupplier.h... Generating docs for file MultithreadedSmilesMolSupplier.h... Generating docs for file new_canon.h... Generating docs for file nmmolhash.h... Generating docs for file Node.h... Generating docs for file Nonbonded.h... Generating docs for file Nonbonded.h... Generating docs for file Normalize.h... Generating docs for file NullQueryAlgebra.h... 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Generating docs for compound MolData3Ddescriptors./build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/DistGeomUtils.h:118: warning: The following parameter of DistGeom::constructForceField(const BoundsMatrix &mmat, RDGeom::PointPtrVect &positions, const VECT_CHIRALSET &csets, double weightChiral=1.0, double weightFourthDim=0.1, std::map< std::pair< int, int >, double > *extraWeights=nullptr, double basinSizeTol=5.0, boost::dynamic_bitset<> *fixedPts=nullptr) is not documented: parameter 'fixedPts' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/ForceField.h:162: warning: argument 'snapshotFreq' of command @param is not found in the argument list of ForceFields::ForceField::minimize(unsigned int maxIts=200, double forceTol=1e-4, double energyTol=1e-6) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/ForceField.h:162: warning: argument 'snapshotVect' of command @param is not found in the argument list of ForceFields::ForceField::minimize(unsigned int maxIts=200, double forceTol=1e-4, double energyTol=1e-6) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/ForceField.h:156: warning: The following parameters of ForceFields::ForceField::minimize(unsigned int snapshotFreq, RDKit::SnapshotVect *snapshotVect, unsigned int maxIts=200, double forceTol=1e-4, double energyTol=1e-6) are not documented: parameter 'snapshotFreq' parameter 'snapshotVect' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/AngleBend.h:31: warning: argument 'angleType' of command @param is not found in the argument list of ForceFields::MMFF::AngleBendContrib::AngleBendContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, const MMFFAngle *mmffAngleParams, const MMFFProp *mmffPropParamsCentralAtom) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/AngleBend.h:40: warning: The following parameters of ForceFields::MMFF::AngleBendContrib::AngleBendContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, const MMFFAngle *mmffAngleParams, const MMFFProp *mmffPropParamsCentralAtom) are not documented: parameter 'mmffAngleParams' parameter 'mmffPropParamsCentralAtom' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/AngleConstraint.h:28: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::MMFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/AngleConstraint.h:28: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::MMFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/AngleConstraint.h:37: warning: The following parameters of ForceFields::MMFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) are not documented: parameter 'minAngleDeg' parameter 'maxAngleDeg' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/BondStretch.h:28: warning: argument 'bondType' of command @param is not found in the argument list of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/BondStretch.h:28: warning: argument 'end1Params' of command @param is not found in the argument list of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/BondStretch.h:28: warning: argument 'end2Params' of command @param is not found in the argument list of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/BondStretch.h:36: warning: The following parameter of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) is not documented: parameter 'mmffBondParams' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/Nonbonded.h:35: warning: The following parameter of ForceFields::MMFF::VdWContrib::VdWContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, const MMFFVdWRijstarEps *mmffVdWConstants) is not documented: parameter 'mmffVdWConstants' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/Nonbonded.h:59: warning: The following parameters of ForceFields::MMFF::EleContrib::EleContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, double chargeTerm, std::uint8_t dielModel, bool is1_4) are not documented: parameter 'chargeTerm' parameter 'dielModel' parameter 'is1_4' .. Generating docs for compound PySequenceHolder... Generating docs for compound SparseBitVect... Generating docs for compound ValueErrorException... Generating namespace index... Generating docs for namespace BFGSOpt Generating docs for namespace boost Generating docs for namespace boost::logging Generating docs for compound boost::logging::rdLogger... Generating docs for namespace boost_adaptbx Generating docs for namespace boost_adaptbx::python Generating docs for compound boost_adaptbx::python::streambuf... Generating docs for nested compound boost_adaptbx::python::streambuf::istream... Generating docs for nested compound boost_adaptbx::python::streambuf::ostream... Generating docs for compound boost_adaptbx::python::streambuf_capsule... Generating docs for compound boost_adaptbx::python::ostream... Generating docs for namespace ChemicalFeatures Generating docs for compound ChemicalFeatures::ChemicalFeature... Generating docs for compound ChemicalFeatures::FreeChemicalFeature... Generating docs for namespace conrec Generating docs for compound conrec::ConrecSegment... Generating docs for namespace DistGeom Generating docs for compound DistGeom::BoundsMatrix... Generating docs for compound DistGeom::ChiralSet... Generating docs for compound DistGeom::ChiralViolationContrib... Generating docs for compound DistGeom::DistViolationContrib... Generating docs for compound DistGeom::FourthDimContrib... Generating docs for namespace ForceFields Generating docs for compound ForceFields::ForceFieldContrib... Generating docs for compound ForceFields::ForceField... Generating docs for namespace ForceFields::CrystalFF Generating docs for compound ForceFields::CrystalFF::TorsionAngleContribM6... Generating docs for compound ForceFields::CrystalFF::CrystalFFDetails... Generating docs for namespace ForceFields::MMFF Generating docs for compound ForceFields::MMFF::AngleBendContrib... Generating docs for compound ForceFields::MMFF::AngleConstraintContrib... Generating docs for compound ForceFields::MMFF::BondStretchContrib... Generating docs for compound ForceFields::MMFF::DistanceConstraintContrib... Generating docs for compound ForceFields::MMFF::VdWContrib... Generating docs for compound ForceFields::MMFF::EleContrib... Generating docs for compound ForceFields::MMFF::OopBendContrib... Generating docs for compound ForceFields::MMFF::MMFFDef... Generating docs for compound ForceFields::MMFF::MMFFProp... Generating docs for compound ForceFields::MMFF::MMFFPBCI... Generating docs for compound ForceFields::MMFF::MMFFChg... Generating docs for compound ForceFields::MMFF::MMFFBond... Generating docs for compound ForceFields::MMFF::MMFFHerschbachLaurie... Generating docs for compound ForceFields::MMFF::MMFFCovRadPauEle... Generating docs for compound ForceFields::MMFF::MMFFAngle... Generating docs for compound ForceFields::MMFF::MMFFStbn... Generating docs for compound ForceFields::MMFF::MMFFOop... Generating docs for compound ForceFields::MMFF::MMFFTor... Generating docs for compound ForceFields::MMFF::MMFFVdW... Generating docs for compound ForceFields::MMFF::MMFFVdWRijstarEps... Generating docs for compound ForceFields::MMFF::MMFFAromCollection... Generating docs for compound ForceFields::MMFF::MMFFDefCollection... Generating docs for compound ForceFields::MMFF::MMFFPropCollection... Generating docs for compound ForceFields::MMFF::MMFFPBCICollection... Generating docs for compound ForceFields::MMFF::MMFFChgCollection... Generating docs for compound ForceFields::MMFF::MMFFBondCollection... Generating docs for compound ForceFields::MMFF::MMFFBndkCollection... Generating docs for compound ForceFields::MMFF::MMFFHerschbachLaurieCollection... Generating docs for compound ForceFields::MMFF::MMFFCovRadPauEleCollection... Generating docs for compound ForceFields::MMFF::MMFFAngleCollection... Generating docs for compound ForceFields::MMFF::MMFFStbnCollection... Generating docs for compound ForceFields::MMFF::MMFFDfsbCollection... Generating docs for compound ForceFields::MMFF::MMFFOopCollection... Generating docs for compound ForceFields::MMFF::M/build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/PositionConstraint.h:29: warning: argument 'minDispl' of command @param is not found in the argument list of ForceFields::MMFF::PositionConstraintContrib::PositionConstraintContrib(ForceField *owner, unsigned int idx, double maxDispl, double forceConst) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/StretchBend.h:32: warning: argument 'angleType' of command @param is not found in the argument list of ForceFields::MMFF::StretchBendContrib::StretchBendContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const MMFFStbn *mmffStbnParams, const MMFFAngle *mmffAngleParams, const MMFFBond *mmffBondParams1, const MMFFBond *mmffBondParams2) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/StretchBend.h:41: warning: The following parameters of ForceFields::MMFF::StretchBendContrib::StretchBendContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const MMFFStbn *mmffStbnParams, const MMFFAngle *mmffAngleParams, const MMFFBond *mmffBondParams1, const MMFFBond *mmffBondParams2) are not documented: parameter 'mmffStbnParams' parameter 'mmffAngleParams' parameter 'mmffBondParams1' parameter 'mmffBondParams2' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/TorsionAngle.h:35: warning: argument 'torsionType' of command @param is not found in the argument list of ForceFields::MMFF::TorsionAngleContrib::TorsionAngleContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, const MMFFTor *mmffTorParams) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF/TorsionAngle.h:46: warning: The following parameter of ForceFields::MMFF::TorsionAngleContrib::TorsionAngleContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, const MMFFTor *mmffTorParams) is not documented: parameter 'mmffTorParams' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/AngleConstraint.h:28: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::UFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/AngleConstraint.h:28: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::UFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/AngleConstraint.h:37: warning: The following parameters of ForceFields::UFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) are not documented: parameter 'minAngleDeg' parameter 'maxAngleDeg' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/Inversion.h:39: warning: The following parameter of ForceFields::UFF::InversionContrib::InversionContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, int at2AtomicNum, bool isCBoundToO, double oobForceScalingFactor=1.0) is not documented: parameter 'oobForceScalingFactor' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF/PositionConstraint.h:29: warning: argument 'minDispl' of command @param is not found in the argument list of ForceFields::UFF::PositionConstraintContrib::PositionConstraintContrib(ForceField *owner, unsigned int idx, double maxDispl, double forceConst) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor/RDDepictor.h:72: warning: The following parameter of RDDepict::compute2DCoords(RDKit::ROMol &mol, const RDGeom::INT_POINT2D_MAP *coordMap=nullptr, bool canonOrient=false, bool clearConfs=true, unsigned int nFlipsPerSample=0, unsigned int nSamples=0, int sampleSeed=0, bool permuteDeg4Nodes=false, bool forceRDKit=false) is not documented: parameter 'forceRDKit' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor/RDDepictor.h:127: warning: The following parameter of RDDepict::compute2DCoordsMimicDistMat(RDKit::ROMol &mol, const DOUBLE_SMART_PTR *dmat=nullptr, bool canonOrient=true, bool clearConfs=true, double weightDistMat=0.5, unsigned int nFlipsPerSample=3, unsigned int nSamples=100, int sampleSeed=25, bool permuteDeg4Nodes=true, bool forceRDKit=false) is not documented: parameter 'forceRDKit' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor/RDDepictor.h:159: warning: The following parameter of RDDepict::generateDepictionMatching2DStructure(RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId=-1, RDKit::ROMol *referencePattern=static_cast< RDKit::ROMol * >(nullptr), bool acceptFailure=false, bool forceRDKit=false) is not documented: parameter 'forceRDKit' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor/RDDepictor.h:167: warning: argument 'refPattern' of command @param is not found in the argument list of RDDepict::generateDepictionMatching3DStructure(RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId=-1, RDKit::ROMol *referencePattern=nullptr, bool acceptFailure=false, bool forceRDKit=false) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor/RDDepictor.h:186: warning: The following parameters of RDDepict::generateDepictionMatching3DStructure(RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId=-1, RDKit::ROMol *referencePattern=nullptr, bool acceptFailure=false, bool forceRDKit=false) are not documented: parameter 'referencePattern' parameter 'forceRDKit' MFFTorCollection... Generating docs for compound ForceFields::MMFF::MMFFVdWCollection... Generating docs for compound ForceFields::MMFF::PositionConstraintContrib... Generating docs for compound ForceFields::MMFF::StretchBendContrib... Generating docs for compound ForceFields::MMFF::TorsionAngleContrib... Generating docs for compound ForceFields::MMFF::TorsionConstraintContrib... Generating docs for namespace ForceFields::MMFF::Utils Generating docs for namespace ForceFields::UFF Generating docs for compound ForceFields::UFF::AngleBendContrib... Generating docs for compound ForceFields::UFF::AngleConstraintContrib... Generating docs for compound ForceFields::UFF::BondStretchContrib... Generating docs for compound ForceFields::UFF::DistanceConstraintContrib... Generating docs for compound ForceFields::UFF::InversionContrib... Generating docs for compound ForceFields::UFF::vdWContrib... Generating docs for compound ForceFields::UFF::UFFBond... Generating docs for compound ForceFields::UFF::UFFAngle... Generating docs for compound ForceFields::UFF::UFFTor... Generating docs for compound ForceFields::UFF::UFFInv... Generating docs for compound ForceFields::UFF::UFFVdW... Generating docs for compound ForceFields::UFF::AtomicParams... Generating docs for compound ForceFields::UFF::ParamCollection... Generating docs for compound ForceFields::UFF::PositionConstraintContrib... Generating docs for compound ForceFields::UFF::TorsionAngleContrib... Generating docs for compound ForceFields::UFF::TorsionConstraintContrib... Generating docs for namespace ForceFields::UFF::Params Generating docs for namespace ForceFields::UFF::Utils Generating docs for namespace Invar Generating docs for compound Invar::Invariant... Generating docs for namespace MolTransforms Generating docs for namespace Queries Generating docs for compound Queries::AndQuery... Generating docs for compound Queries::EqualityQuery... Generating docs for compound Queries::GreaterEqualQuery... Generating docs for compound Queries::GreaterQuery... Generating docs for compound Queries::LessEqualQuery... Generating docs for compound Queries::LessQuery... Generating docs for compound Queries::OrQuery... Generating docs for compound Queries::Int2Type... Generating docs for compound Queries::Query... Generating docs for compound Queries::RangeQuery... Generating docs for compound Queries::SetQuery... Generating docs for compound Queries::XOrQuery... Generating docs for namespace Rankers Generating docs for compound Rankers::pairGreater... Generating docs for compound Rankers::pairLess... Generating docs for compound Rankers::argless... Generating docs for namespace RDCatalog Generating docs for compound RDCatalog::Catalog... Generating docs for compound RDCatalog::HierarchCatalog... Generating docs for nested compound RDCatalog::HierarchCatalog::vertex_entry_t... Generating docs for compound RDCatalog::CatalogEntry... Generating docs for compound RDCatalog::CatalogParams... Generating docs for namespace RDDataManip Generating docs for compound RDDataManip::MetricMatrixCalc... Generating docs for namespace RDDepict Generating docs for compound RDDepict::gtIIPair... Generating docs for compound RDDepict::EmbeddedAtom... Generating docs for compound RDDepict::EmbeddedFrag... Generating docs for compound RDDepict::DepictException... Generating docs for namespace RDFeatures Generating docs for compound RDFeatures::ExplicitFeature... Generating docs for compound RDFeatures::ImplicitFeature... Generating docs for namespace RDGeom Generating docs for compound RDGeom::GridException... Generating docs for compound RDGeom::Grid3D... Generating docs for compound RDGeom::Point... Generating docs for compound RDGeom::Point3D... Generating docs for compound RDGeom::Point2D... Generating docs for compound RDGeom::PointND... Generating docs for compound RDGeom::Transform2D... Generating docs for compound RDGeom::Transform3D... Generating docs for compound RDGeom::UniformGrid3D... Generating docs for namespace RDInfoTheory Generating docs for compound RDInfoTheory::BitCorrMatGenerator... Generati/build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/QueryOps.h:515: warning: Found unknown command '\overloadquery' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/QueryOps.h:524: warning: Found unknown command '\overloadquery' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstanceGroup.h:231: warning: The following parameter of RDKit::addSubstanceGroup(ROMol &mol, SubstanceGroup sgroup) is not documented: parameter 'mol' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/SequenceParsers.h:105: warning: argument 'seq' of command @param is not found in the argument list of RDKit::HELMToMol(const char *helm, bool sanitize=true) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/SequenceParsers.h:110: warning: The following parameter of RDKit::HELMToMol(const char *helm, bool sanitize=true) is not documented: parameter 'helm' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/Fingerprints.h:105: warning: The following parameter of RDKit::LayeredFingerprintMol(const ROMol &mol, unsigned int layerFlags=0xFFFFFFFF, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=nullptr, ExplicitBitVect *setOnlyBits=nullptr, bool branchedPaths=true, const std::vector< std::uint32_t > *fromAtoms=nullptr) is not documented: parameter 'fromAtoms' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/QueryOps.h:515: warning: Found unknown command '\overloadquery' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/QueryOps.h:524: warning: Found unknown command '\overloadquery' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/FileParsers.h:60: warning: argument 'line' from the argument list of RDKit::MolDataStreamToMol has multiple @param documentation sections /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesWrite.h:152: warning: argument 'doRandom' of command @param is not found in the argument list of RDKit::MolFragmentToCXSmiles(const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, const std::vector< std::string > *atomSymbols=nullptr, const std::vector< std::string > *bondSymbols=nullptr, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesWrite.h:99: warning: argument 'doRandom' of command @param is not found in the argument list of RDKit::MolFragmentToSmiles(const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, const std::vector< std::string > *atomSymbols=nullptr, const std::vector< std::string > *bondSymbols=nullptr, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesWrite.h:145: warning: The following parameter of RDKit::MolToCXSmiles(const ROMol &mol, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false, bool doRandom=false) is not documented: parameter 'doRandom' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/FileParsers.h:318: warning: argument 'fName' of command @param is not found in the argument list of RDKit::MolToPDBFile(const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers/FileParsers.h:329: warning: The following parameter of RDKit::MolToPDBFile(const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0) is not documented: parameter 'fname' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesWrite.h:74: warning: The following parameter of RDKit::MolToSmiles(const ROMol &mol, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false, bool doRandom=false) is not documented: parameter 'doRandom' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/Fingerprints.h:144: warning: The following parameter of RDKit::PatternFingerprintMol(const ROMol &mol, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=nullptr, ExplicitBitVect *setOnlyBits=nullptr, bool tautomericFingerprint=false) is not documented: parameter 'tautomericFingerprint' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/Fingerprints.h:26: warning: argument 'useBondOrders' of command @param is not found in the argument list of RDKit::RDKFingerprintMol(const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=2, bool useHs=true, double tgtDensity=0.0, unsigned int minSize=128, bool branchedPaths=true, bool useBondOrder=true, std::vector< std::uint32_t > *atomInvariants=nullptr, const std::vector< std::uint32_t > *fromAtoms=nullptr, std::vector< std::vector< std::uint32_t >> *atomBits=nullptr, std::map< std::uint32_t, std::vector< std::vector< int >>> *bitInfo=nullptr) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/Fingerprints.h:53: warning: The following parameters of RDKit::RDKFingerprintMol(const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=2, bool useHs=true, double tgtDensity=0.0, unsigned int minSize=128, bool branchedPaths=true, bool useBondOrder=true, std::vector< std::uint32_t > *atomInvariants=nullptr, const std::vector< std::uint32_t > *fromAtoms=nullptr, std::vector< std::vector< std::uint32_t >> *atomBits=nullptr, std::map< std::uint32_t, std::vector< std::vector< int >>> *bitInfo=nullptr) are not documented: parameter 'useBondOrder' parameter 'bitInfo' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionRunner.h:97: warning: The following parameter of RDKit::reduceProductToSideChains(const ROMOL_SPTR &product, bool addDummyAtoms=true) is not documented: parameter 'product' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemTransforms/ChemTransforms.h:114: warning: argument 'useChirality' of command @param is not found in the argument list of RDKit::replaceCore(const ROMol &mol, const ROMol &core, const MatchVectType &matchVect, bool replaceDummies=true, bool labelByIndex=false, bool requireDummyMatch=false) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionRunner.h:64: warning: argument 'reactantTemplateIdx' of command @param is not found in the argument list of RDKit::run_Reactant(const ChemicalReaction &rxn, const ROMOL_SPTR &reactant, unsigned int reactantIdx) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionRunner.h:77: warning: The following parameters of RDKit::run_Reactant(const ChemicalReaction &rxn, const ROMOL_SPTR &reactant, unsigned int reactantIdx) are not documented: parameter 'rxn' parameter 'reactantIdx' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Substruct/SubstructMatch.h:56: warning: argument 'matchParams' of command @param is not found in the argument list of RDKit::SubstructMatch(const ROMol &mol, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters()) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Substruct/SubstructMatch.h:63: warning: The following parameter of RDKit::SubstructMatch(const ROMol &mol, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters()) is not documented: parameter 'params' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Substruct/SubstructMatch.h:69: warning: argument 'matchParams' of command @param is not found in the argument list of RDKit::SubstructMatch(ResonanceMolSupplier &resMolSuppl, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters()) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Substruct/SubstructMatch.h:76: warning: The following parameter of RDKit::SubstructMatch(ResonanceMolSupplier &resMolSuppl, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters()) is not documented: parameter 'params' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Substruct/SubstructMatch.h:145: warning: The following parameter of RDKit::SubstructMatch(T1 &mol, const T2 &query, std::vector< MatchVectType > &matchVect, bool uniquify=true, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false, unsigned int maxMatches=1000, int numThreads=1) is not documented: parameter 'numThreads' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Reaction.h:207: warning: argument 'maxProducts' of command @param is not found in the argument list of RDKit::ChemicalReaction::runReactants(const MOL_SPTR_VECT reactants, unsigned int numProducts=1000) const /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Reaction.h:219: warning: The following parameter of RDKit::ChemicalReaction::runReactants(const MOL_SPTR_VECT reactants, unsigned int numProducts=1000) const is not documented: parameter 'numProducts' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:99: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatcherBase::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const=0 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:105: warning: The following parameter of RDKit::FilterMatcherBase::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const=0 is not documented: parameter 'matchVect' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:322: warning: argument 'matches' of command @param is not found in the argument list of RDKit::SmartsMatcher::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 99 in file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:322: warning: The following parameter of RDKit::SmartsMatcher::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:415: warning: argument 'matches' of command @param is not found in the argument list of RDKit::ExclusionList::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 99 in file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:415: warning: The following parameter of RDKit::ExclusionList::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/FingerprintGenerator.h:109: warning: The following parameter of RDKit::AtomEnvironment::getBitId(FingerprintArguments< OutputType > *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, const AdditionalOutput *AdditionalOutput, const bool hashResults=false) const=0 is not documented: parameter 'AdditionalOutput' ng docs for compound RDInfoTheory::InfoBitRanker... Generating docs for namespace RDKit Generating docs for compound RDKit::Atom... Generating docs for compound RDKit::atomicData... Generating docs for compound RDKit::AtomIterator_... Generating docs for compound RDKit::HeteroatomIterator_... Generating docs for compound RDKit::AromaticAtomIterator_... Generating docs for compound RDKit::QueryAtomIterator_... Generating docs for compound RDKit::MatchingAtomIterator_... Generating docs for compound RDKit::Bond... Generating docs for compound RDKit::BondIterator_... Generating docs for compound RDKit::ConstBondIterator_... Generating docs for compound RDKit::CartesianProductStrategy... Generating docs for compound RDKit::EnumerationParams... Generating docs for compound RDKit::EnumerateLibrary... Generating docs for compound RDKit::EnumerateLibraryBase... Generating docs for compound RDKit::EnumerationStrategyException... Generating docs for compound RDKit::EnumerationStrategyBase... Generating docs for compound RDKit::EvenSamplePairsStrategy... Generating docs for compound RDKit::RandomSampleStrategy... Generating docs for compound RDKit::RandomSampleAllBBsStrategy... Generating docs for compound RDKit::ChemicalReactionException... Generating docs for compound RDKit::ChemicalReaction... Generating docs for compound RDKit::ReactionFingerprintParams... Generating docs for compound RDKit::ChemicalReactionParserException... Generating docs for compound RDKit::ReactionPicklerException... Generating docs for compound RDKit::ReactionPickler... Generating docs for compound RDKit::RxnSanitizeException... Generating docs for compound RDKit::ConformerException... Generating docs for compound RDKit::Conformer... Generating docs for compound RDKit::MolFileUnhandledFeatureException... Generating docs for compound RDKit::MolSupplier... Generating docs for compound RDKit::ForwardSDMolSupplier... Generating docs for compound RDKit::SDMolSupplier... Generating docs for compound RDKit::SmilesMolSupplier... Generating docs for compound RDKit::TDTMolSupplier... Generating docs for compound RDKit::PDBMolSupplier... Generating docs for compound RDKit::MolWriter... Generating docs for compound RDKit::SmilesWriter... Generating docs for compound RDKit::SDWriter... Generating docs for compound RDKit::TDTWriter... Generating docs for compound RDKit::PDBWriter... Generating docs for compound RDKit::FilterCatalogParams... Generating docs for compound RDKit::FilterCatalog... Generating docs for compound RDKit::FilterCatalogEntry... Generating docs for compound RDKit::FilterMatch... Generating docs for compound RDKit::FilterMatcherBase... Generating docs for compound RDKit::SmartsMatcher... Generating docs for compound RDKit::ExclusionList... Generating docs for compound RDKit::FilterHierarchyMatcher... Generating docs for compound RDKit::FilterData_t... Generating docs for compound RDKit::FilterProperty_t... Generating docs for compound RDKit::AdditionalOutput... Generating docs for compound RDKit::FingerprintArguments... Generating docs for compound RDKit::AtomEnvironment... Generating docs for compound RDKit::AtomEnvironmentGenerator... Generating docs for compound RDKit::AtomInvariantsGenerator... Generating docs for compound RDKit::BondInvariantsGenerator... Generating docs for compound RDKit::FingerprintGenerator... Generating docs for compound RDKit::UnimplementedFPException... Generating docs for compound RDKit::MCSAtomCompareParameters... Generating docs for compound RDKit::MCSBondCompareParameters... Generating docs for compound RDKit::MCSProgressData... Generating docs for compound RDKit::MCSParameters... Generating docs for compound RDKit::MCSResult... Generating docs for compound RDKit::FragCatalogEntry... Generating docs for compound RDKit::FragCatGenerator... Generating docs for compound RDKit::FragCatParams... Generating docs for compound RDKit::FragFPGenerator... Generating docs for compound RDKit::MolBundle... Generating docs for compound RDKit::FixedMolSizeMolBundle... Generating docs for compound RDKit::MolCatalogEntry... Generating/build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:334: warning: argument 'highlight_atoms' from the argument list of RDKit::MolDraw2D::drawMolecule has multiple @param documentation sections /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:334: warning: The following parameter of RDKit::MolDraw2D::drawMolecule(const ROMol &mol, const std::string &legend, const std::vector< int > *highlight_atoms, const std::vector< int > *highlight_bonds, const std::map< int, DrawColour > *highlight_atom_map=nullptr, const std::map< int, DrawColour > *highlight_bond_map=nullptr, const std::map< int, double > *highlight_radii=nullptr, int confId=-1) is not documented: parameter 'highlight_bonds' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:387: warning: argument 'highlight_atom_map' of command @param is not found in the argument list of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int >> *highlight_atoms=nullptr, const std::vector< std::vector< int >> *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour >> *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour >> *highlight_bond_maps=nullptr, const std::vector< std::map< int, double >> *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:387: warning: argument 'highlight_bond_map' of command @param is not found in the argument list of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int >> *highlight_atoms=nullptr, const std::vector< std::vector< int >> *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour >> *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour >> *highlight_bond_maps=nullptr, const std::vector< std::map< int, double >> *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:387: warning: argument 'confId' of command @param is not found in the argument list of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int >> *highlight_atoms=nullptr, const std::vector< std::vector< int >> *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour >> *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour >> *highlight_bond_maps=nullptr, const std::vector< std::map< int, double >> *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:411: warning: argument 'highlight_atoms' from the argument list of RDKit::MolDraw2D::drawMolecules has multiple @param documentation sections /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:411: warning: The following parameters of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int >> *highlight_atoms=nullptr, const std::vector< std::vector< int >> *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour >> *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour >> *highlight_bond_maps=nullptr, const std::vector< std::map< int, double >> *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr) are not documented: parameter 'highlight_bonds' parameter 'highlight_atom_maps' parameter 'highlight_bond_maps' parameter 'confIds' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:377: warning: The following parameter of RDKit::MolDraw2D::drawMoleculeWithHighlights(const ROMol &mol, const std::string &legend, const std::map< int, std::vector< DrawColour >> &highlight_atom_map, const std::map< int, std::vector< DrawColour >> &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) is not documented: parameter 'highlight_linewidth_multipliers' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Resonance.h:114: warning: argument 'numThreads' of command @param is not found in the argument list of RDKit::ResonanceMolSupplier::ResonanceMolSupplier(ROMol &mol, unsigned int flags=0, unsigned int maxStructs=1000) docs for compound RDKit::MolCatalogParams... Generating docs for compound RDKit::FeatureFileParseException... Generating docs for compound RDKit::MolChemicalFeature... Generating docs for compound RDKit::MolChemicalFeatureDef... Generating docs for compound RDKit::MolChemicalFeatureFactory... Generating docs for compound RDKit::DrawText... Generating docs for compound RDKit::DrawTextCairo... Generating docs for compound RDKit::DrawTextFT... Generating docs for compound RDKit::DrawTextFTCairo... Generating docs for compound RDKit::DrawTextFTJS... Generating docs for compound RDKit::DrawTextFTQt... Generating docs for compound RDKit::DrawTextFTSVG... Generating docs for compound RDKit::DrawTextJS... Generating docs for compound RDKit::DrawTextQt... Generating docs for compound RDKit::DrawTextSVG... Generating docs for compound RDKit::DrawColour... Generating docs for compound RDKit::StringRect... Generating docs for compound RDKit::MolDrawOptions... Generating docs for compound RDKit::MolDraw2D... Generating docs for compound RDKit::MolDraw2DCairo... Generating docs for compound RDKit::MolDraw2DJS... Generating docs for compound RDKit::MolDraw2DQt... Generating docs for compound RDKit::MolDraw2DSVG... Generating docs for compound RDKit::MolDraw2Dwx... Generating docs for compound RDKit::MultiMolDraw2D... Generating docs for compound RDKit::MolPicklerException... Generating docs for compound RDKit::MolPickler... Generating docs for compound RDKit::AtomMonomerInfo... Generating docs for compound RDKit::AtomPDBResidueInfo... Generating docs for compound RDKit::GasteigerParams... Generating docs for compound RDKit::PeriodicTable... Generating docs for compound RDKit::QueryAtom... Generating docs for compound RDKit::QueryBond... Generating docs for compound RDKit::AtomRingQuery... Generating docs for compound RDKit::RecursiveStructureQuery... Generating docs for compound RDKit::HasPropQuery... Generating docs for compound RDKit::HasPropWithValueQuery... Generating docs for compound RDKit::HasPropWithValueQuery< TargetPtr, std::string >... Generating docs for compound RDKit::HasPropWithValueQuery< TargetPtr, ExplicitBitVect >... Generating docs for compound RDKit::ResonanceMolSupplierCallback... Generating docs for compound RDKit::ResonanceMolSupplier... Generating docs for compound RDKit::RCore... Generating docs for compound RDKit::RGroupData... Generating docs for compound RDKit::RGroupDecompositionParameters... Generating docs for compound RDKit::RGroupDecomposition... Generating docs for compound RDKit::RGroupDecompData... Generating docs for nested compound RDKit::RGroupDecompData::UsedLabels... Generating docs for compound RDKit::RGroupMatch... Generating docs for compound RDKit::CartesianProduct... Generating docs for compound RDKit::RingInfo... Generating docs for compound RDKit::CXXAtomIterator... Generating docs for nested compound RDKit::CXXAtomIterator::CXXAtomIter... Generating docs for compound RDKit::CXXBondIterator... Generating docs for nested compound RDKit::CXXBondIterator::CXXBondIter... Generating docs for compound RDKit::ROMol... Generating docs for compound RDKit::RWMol... Generating docs for compound RDKit::MolSanitizeException... Generating docs for compound RDKit::AtomSanitizeException... Generating docs for compound RDKit::AtomValenceException... Generating docs for compound RDKit::AtomKekulizeException... Generating docs for compound RDKit::KekulizeException... Generating docs for compound RDKit::SLNParseException... Generating docs for compound RDKit::SmilesParserParams... Generating docs for compound RDKit::SmilesParseException... Generating docs for compound RDKit::StereoGroup... Generating docs for compound RDKit::SubstanceGroupException... Generating docs for compound RDKit::SubstanceGroup... Generating docs for nested compound RDKit::SubstanceGroup::AttachPoint... Generating docs for nested compound RDKit::SubstanceGroup::CState... Generating docs for compound RDKit::SubstructMatchParameters... Generating docs for compound RDKit::MolHolderBase... Generating docs for compound RDKit::MolHolder../build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Abbreviations/Abbreviations.h:105: warning: The following parameter of RDKit::Abbreviations::findApplicableAbbreviationMatches(const ROMol &mol, const std::vector< AbbreviationDefinition > &abbrevs, double maxCoverage=0.4) is not documented: parameter 'mol' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/AtomPairGenerator.h:103: warning: The following parameter of RDKit::AtomPair::AtomPairAtomEnv::getBitId(FingerprintArguments< OutputType > *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, const AdditionalOutput *AdditionalOutput, const bool hashResults=false) const is not documented: parameter 'AdditionalOutput' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/AtomPairs.h:121: warning: The following parameter of RDKit::AtomPairs::getHashedAtomPairFingerprint(const ROMol &mol, unsigned int nBits=2048, unsigned int minLength=1, unsigned int maxLength=maxPathLen - 1, const std::vector< std::uint32_t > *fromAtoms=nullptr, const std::vector< std::uint32_t > *ignoreAtoms=nullptr, const std::vector< std::uint32_t > *atomInvariants=nullptr, bool includeChirality=false, bool use2D=true, int confId=-1) is not documented: parameter 'confId' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/FingerprintUtil.h:77: warning: The following parameter of RDKit::AtomPairs::getTopologicalTorsionCode(const std::vector< std::uint32_t > &atomCodes, bool includeChirality=false) is not documented: parameter 'includeChirality' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Canon.h:114: warning: The following parameters of RDKit::Canon::canonicalizeFragment(ROMol &mol, int atomIdx, std::vector< AtomColors > &colors, const std::vector< unsigned int > &ranks, MolStack &molStack, const boost::dynamic_bitset<> *bondsInPlay=nullptr, const std::vector< std::string > *bondSymbols=nullptr, bool doIsomericSmiles=false, bool doRandom=false) are not documented: parameter 'bondsInPlay' parameter 'bondSymbols' parameter 'doIsomericSmiles' parameter 'doRandom' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Chirality.h:106: warning: The following parameter of RDKit::Chirality::findPotentialStereo(ROMol &mol, bool cleanIt, bool flagPossible=true) is not documented: parameter 'flagPossible' . Generating docs for compound RDKit::CachedMolHolder... Generating docs for compound RDKit::CachedSmilesMolHolder... Generating docs for compound RDKit::CachedTrustedSmilesMolHolder... Generating docs for compound RDKit::FPHolderBase... Generating docs for compound RDKit::PatternHolder... Generating docs for compound RDKit::SubstructLibrary... Generating docs for compound RDKit::TautomerQuery... Generating docs for compound RDKit::Snapshot... Generating docs for compound RDKit::Trajectory... Generating docs for compound RDKit::DataStructsExplicitBitVecPropHandler... Generating docs for compound RDKit::DiscreteDistMat... Generating docs for compound RDKit::DiscreteValueVect... Generating docs for compound RDKit::FPBReader... Generating docs for compound RDKit::MultiFPBReader... Generating docs for compound RDKit::SparseIntVect... Generating docs for compound RDKit::BadFileException... Generating docs for compound RDKit::Dict... Generating docs for nested compound RDKit::Dict::Pair... Generating docs for compound RDKit::FileParseException... Generating docs for compound RDKit::RDAny... Generating docs for compound RDKit::RDProps... Generating docs for compound RDKit::RDValue... Generating docs for compound RDKit::CustomPropHandler... Generating docs for compound RDKit::ltDouble... Generating docs for compound RDKit::larger_of... Generating docs for compound RDKit::charptr_functor... Generating docs for namespace RDKit::Abbreviations Generating docs for compound RDKit::Abbreviations::AbbreviationDefinition... Generating docs for compound RDKit::Abbreviations::AbbreviationMatch... Generating docs for namespace RDKit::Abbreviations::common_properties Generating docs for namespace RDKit::Abbreviations::Utils Generating docs for namespace RDKit::AtomPair Generating docs for compound RDKit::AtomPair::AtomPairAtomInvGenerator... Generating docs for compound RDKit::AtomPair::AtomPairArguments... Generating docs for compound RDKit::AtomPair::AtomPairAtomEnv... Generating docs for compound RDKit::AtomPair::AtomPairEnvGenerator... Generating docs for namespace RDKit::AtomPairs Generating docs for namespace RDKit::Canon Generating docs for compound RDKit::Canon::MolStackUnion... Generating docs for compound RDKit::Canon::MolStackElem... Generating docs for compound RDKit::Canon::bondholder... Generating docs for compound RDKit::Canon::canon_atom... Generating docs for compound RDKit::Canon::SpecialChiralityAtomCompareFunctor... Generating docs for compound RDKit::Canon::SpecialSymmetryAtomCompareFunctor... Generating docs for compound RDKit::Canon::AtomCompareFunctor... Generating docs for compound RDKit::Canon::ChiralAtomCompareFunctor... Generating docs for namespace RDKit::Chirality Generating docs for compound RDKit::Chirality::StereoInfo... Generating docs for namespace RDKit::CIPLabeler Generating docs for compound RDKit::CIPLabeler::CIPMolSpan... Generating docs for nested compound RDKit::CIPLabeler::CIPMolSpan::CIPMolIter... Generating docs for compound RDKit::CIPLabeler::CIPMol... Generating docs for compound RDKit::CIPLabeler::Configuration... Generating docs for compound RDKit::CIPLabeler::Sp2Bond... Generating docs for compound RDKit::CIPLabeler::Tetrahedral... Generating docs for compound RDKit::CIPLabeler::Digraph... Generating docs for compound RDKit::CIPLabeler::Edge... Generating docs for compound RDKit::CIPLabeler::Node... Generating docs for compound RDKit::CIPLabeler::Priority... Generating docs for compound RDKit::CIPLabeler::PairList... Generating docs for compound RDKit::CIPLabeler::Rule1a... Generating docs for compound RDKit::CIPLabeler::Rule1b... Generating docs for compound RDKit::CIPLabeler::Rule2... Generating docs for compound RDKit::CIPLabeler::Rule3... Generating docs for compound RDKit::CIPLabeler::Rule4a... Generating docs for compound RDKit::CIPLabeler::Rule4b... Generating docs for compound RDKit::CIPLabeler::Rule4c... Generating docs for compound RDKit::CIPLabeler::Rule5... Generating docs for compound RDKit::CIPLabeler::Rule5New... Generating docs for compound RDKit::CIPLabeler::Rule6... Generati/build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/Lipinski.h:45: warning: argument 'strict' of command @param is not found in the argument list of RDKit::Descriptors::calcNumRotatableBonds(const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/Lipinski.h:52: warning: The following parameter of RDKit::Descriptors::calcNumRotatableBonds(const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default) is not documented: parameter 'useStrictDefinition' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/USRDescriptor.h:81: warning: The following parameter of RDKit::Descriptors::USRCAT(const ROMol &mol, std::vector< double > &descriptor, std::vector< std::vector< unsigned int >> &atomIds, int confId=-1) is not documented: parameter 'atomIds' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:86: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatchOps::And::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 99 in file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:86: warning: The following parameter of RDKit::FilterMatchOps::And::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:148: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatchOps::Or::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 99 in file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:148: warning: The following parameter of RDKit::FilterMatchOps::Or::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:204: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatchOps::Not::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 99 in file /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:204: warning: The following parameter of RDKit::FilterMatchOps::Not::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MHFP.h:104: warning: found tag without matching /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MHFP.h:116: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::CreateShingling(const ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=true, unsigned char min_radius=1) is not documented: parameter 'mol' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MHFP.h:144: warning: found tag without matching /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MHFP.h:156: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::Encode(ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=true, unsigned char min_radius=1) is not documented: parameter 'mol' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MHFP.h:202: warning: found tag without matching /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MHFP.h:216: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::EncodeSECFP(ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=true, unsigned char min_radius=1, size_t length=2048) is not documented: parameter 'mol' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MMPA/MMPA.h:36: warning: The following parameter of RDKit::MMPA::fragmentMol(const ROMol &mol, std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR >> &result, unsigned int maxCuts=3, unsigned int maxCutBonds=20, const std::string &pattern="[#6+0;!$(*=,#[!#6])]!@!=!#[*]") is not documented: parameter 'pattern' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MMPA/MMPA.h:57: warning: The following parameter of RDKit::MMPA::fragmentMol(const ROMol &mol, std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR >> &result, unsigned int minCuts, unsigned int maxCuts, unsigned int maxCutBonds, const std::string &pattern="[#6+0;!$(*=,#[!#6])]!@!=!#[*]") is not documented: parameter 'pattern' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign/AlignMolecules.h:136: warning: argument 'probeId' of command @param is not found in the argument list of RDKit::MolAlign::CalcRMS(ROMol &probeMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6, const RDNumeric::DoubleVector *weights=nullptr) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign/AlignMolecules.h:136: warning: argument 'refId' of command @param is not found in the argument list of RDKit::MolAlign::CalcRMS(ROMol &probeMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6, const RDNumeric::DoubleVector *weights=nullptr) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign/AlignMolecules.h:155: warning: The following parameters of RDKit::MolAlign::CalcRMS(ROMol &probeMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6, const RDNumeric::DoubleVector *weights=nullptr) are not documented: parameter 'prbCid' parameter 'refCid' ng docs for compound RDKit::CIPLabeler::Rules... Generating docs for compound RDKit::CIPLabeler::SequenceRule... Generating docs for compound RDKit::CIPLabeler::Sort... Generating docs for compound RDKit::CIPLabeler::TooManyNodesException... Generating docs for namespace RDKit::common_properties Generating docs for namespace RDKit::constants Generating docs for namespace RDKit::Deprotect Generating docs for compound RDKit::Deprotect::DeprotectData... Generating docs for namespace RDKit::Descriptors Generating docs for compound RDKit::Descriptors::CrippenParams... Generating docs for compound RDKit::Descriptors::CrippenParamCollection... Generating docs for compound RDKit::Descriptors::PropertyFunctor... Generating docs for compound RDKit::Descriptors::Properties... Generating docs for namespace RDKit::Descriptors::detail Generating docs for namespace RDKit::detail Generating docs for namespace RDKit::DGeomHelpers Generating docs for compound RDKit::DGeomHelpers::EmbedParameters... Generating docs for namespace RDKit::DTags Generating docs for namespace RDKit::EnumerationStrategyPickler Generating docs for namespace RDKit::EnumerationTypes Generating docs for namespace RDKit::FileParserUtils Generating docs for namespace RDKit::FilterMatchOps Generating docs for compound RDKit::FilterMatchOps::And... Generating docs for compound RDKit::FilterMatchOps::Or... Generating docs for compound RDKit::FilterMatchOps::Not... Generating docs for namespace RDKit::FMCS Generating docs for compound RDKit::FMCS::Composition2N... Generating docs for compound RDKit::FMCS::ExecStatistics... Generating docs for compound RDKit::FMCS::DuplicatedSeedCache... Generating docs for nested compound RDKit::FMCS::DuplicatedSeedCache::TKey... Generating docs for compound RDKit::FMCS::Graph... Generating docs for compound RDKit::FMCS::TArray2D... Generating docs for compound RDKit::FMCS::MaximumCommonSubgraph... Generating docs for compound RDKit::FMCS::RingMatchTableSet... Generating docs for compound RDKit::FMCS::MolFragment... Generating docs for compound RDKit::FMCS::NewBond... Generating docs for compound RDKit::FMCS::Seed... Generating docs for compound RDKit::FMCS::SeedSet... Generating docs for compound RDKit::FMCS::SubstructureCache... Generating docs for nested compound RDKit::FMCS::SubstructureCache::HashKey... Generating docs for nested compound RDKit::FMCS::SubstructureCache::KeyNumericMetrics... Generating docs for compound RDKit::FMCS::Target... Generating docs for compound RDKit::FMCS::TargetMatch... Generating docs for namespace RDKit::ForceFieldsHelper Generating docs for namespace RDKit::ForceFieldsHelper::detail Generating docs for namespace RDKit::GeneralMolSupplier Generating docs for compound RDKit::GeneralMolSupplier::SupplierOptions... Generating docs for namespace RDKit::Local Generating docs for namespace RDKit::MACCSFingerprints Generating docs for namespace RDKit::MHFPFingerprints Generating docs for compound RDKit::MHFPFingerprints::MHFPEncoder... Generating docs for namespace RDKit::MHFPFingerprints::FNV Generating docs for namespace RDKit::MMFF Generating docs for compound RDKit::MMFF::MMFFAtomProperties... Generating docs for compound RDKit::MMFF::MMFFMolProperties... Generating docs for namespace RDKit::MMFF::DefaultParameters Generating docs for namespace RDKit::MMFF::Tools Generating docs for compound RDKit::MMFF::Tools::DefaultTorsionBondSmarts... Generating docs for namespace RDKit::MMPA Generating docs for namespace RDKit::MolAlign Generating docs for compound RDKit::MolAlign::MolAlignException... Generating docs for compound RDKit::MolAlign::O3AFuncData... Generating docs for compound RDKit::MolAlign::O3AConstraint... Generating docs for compound RDKit::MolAlign::O3AConstraintVect... Generating docs for compound RDKit::MolAlign::MolHistogram... Generating docs for compound RDKit::MolAlign::LAP... Generating docs for compound RDKit::MolAlign::SDM... Generating docs for compound RDKit::MolAlign::O3A... Generating docs for namespace RDKit::MolDraw2D_detail Generating docs for namespace RDKit::MolDraw2DUtils Generati/build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:70: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:73: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:70: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:73: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:123: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:126: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:130: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:133: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:133: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:123: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:130: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:126: warning: Found unknown command '\override' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolOps.h:749: warning: The following parameter of RDKit::MolOps::getAdjacencyMatrix(const ROMol &mol, bool useBO=false, int emptyVal=0, bool force=false, const char *propNamePrefix=nullptr, const boost::dynamic_bitset<> *bondsToUse=nullptr) is not documented: parameter 'bondsToUse' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolOps.h:302: warning: The following parameter of RDKit::MolOps::mergeQueryHs(const ROMol &mol, bool mergeUnmappedOnly=false) is not documented: parameter 'mergeUnmappedOnly' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.h:191: warning: argument 'OutputType' of command @param is not found in the argument list of RDKit::MorganFingerprint::getMorganGenerator(const unsigned int radius, const bool countSimulation=false, const bool includeChirality=false, const bool useBondTypes=true, const bool onlyNonzeroInvariants=false, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, BondInvariantsGenerator *bondInvariantsGenerator=nullptr, const std::uint32_t fpSize=2048, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const bool ownsAtomInvGen=false, const bool ownsBondInvGen=false) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.h:191: warning: argument 'radiu' of command @param is not found in the argument list of RDKit::MorganFingerprint::getMorganGenerator(const unsigned int radius, const bool countSimulation=false, const bool includeChirality=false, const bool useBondTypes=true, const bool onlyNonzeroInvariants=false, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, BondInvariantsGenerator *bondInvariantsGenerator=nullptr, const std::uint32_t fpSize=2048, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const bool ownsAtomInvGen=false, const bool ownsBondInvGen=false) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.h:228: warning: argument 'countSimulation' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.h:228: warning: argument 'includeChirality' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.h:228: warning: argument 'onlyNonzeroInvariants' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.h:228: warning: The following parameter of RDKit::MorganFingerprint::getMorganGenerator(const unsigned int radius, const bool countSimulation=false, const bool includeChirality=false, const bool useBondTypes=true, const bool onlyNonzeroInvariants=false, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, BondInvariantsGenerator *bondInvariantsGenerator=nullptr, const std::uint32_t fpSize=2048, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const bool ownsAtomInvGen=false, const bool ownsBondInvGen=false) is not documented: parameter 'radius' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.h:151: warning: The following parameter of RDKit::MorganFingerprint::MorganAtomEnv::getBitId(FingerprintArguments< OutputType > *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, const AdditionalOutput *AdditionalOutput, const bool hashResults=false) const is not documented: parameter 'AdditionalOutput' ng docs for compound RDKit::MolDraw2DUtils::ContourParams... Generating docs for namespace RDKit::MolEnumerator Generating docs for compound RDKit::MolEnumerator::MolEnumeratorOp... Generating docs for compound RDKit::MolEnumerator::PositionVariationOp... Generating docs for compound RDKit::MolEnumerator::LinkNodeOp... Generating docs for compound RDKit::MolEnumerator::MolEnumeratorParams... Generating docs for namespace RDKit::MolFragmenter Generating docs for compound RDKit::MolFragmenter::FragmenterBondType... Generating docs for namespace RDKit::MolHash Generating docs for namespace RDKit::MolInterchange Generating docs for compound RDKit::MolInterchange::JSONParseParameters... Generating docs for namespace RDKit::MolOps Generating docs for compound RDKit::MolOps::RemoveHsParameters... Generating docs for compound RDKit::MolOps::AdjustQueryParameters... Generating docs for namespace RDKit::MolShapes Generating docs for namespace RDKit::MolStandardize Generating docs for compound RDKit::MolStandardize::AcidBaseCatalogEntry... Generating docs for compound RDKit::MolStandardize::AcidBaseCatalogParams... Generating docs for compound RDKit::MolStandardize::ChargeCorrection... Generating docs for compound RDKit::MolStandardize::Reionizer... Generating docs for compound RDKit::MolStandardize::Uncharger... Generating docs for compound RDKit::MolStandardize::FragmentRemover... Generating docs for compound RDKit::MolStandardize::LargestFragmentChooser... Generating docs for nested compound RDKit::MolStandardize::LargestFragmentChooser::Largest... Generating docs for compound RDKit::MolStandardize::FragmentCatalogEntry... Generating docs for compound RDKit::MolStandardize::FragmentCatalogParams... Generating docs for compound RDKit::MolStandardize::MetalDisconnector... Generating docs for compound RDKit::MolStandardize::CleanupParameters... Generating docs for compound RDKit::MolStandardize::Normalizer... Generating docs for compound RDKit::MolStandardize::Tautomer... Generating docs for compound RDKit::MolStandardize::TautomerEnumeratorResult... Generating docs for nested compound RDKit::MolStandardize::TautomerEnumeratorResult::const_iterator... Generating docs for compound RDKit::MolStandardize::TautomerEnumeratorCallback... Generating docs for compound RDKit::MolStandardize::TautomerEnumerator... Generating docs for compound RDKit::MolStandardize::TautomerCatalogEntry... Generating docs for compound RDKit::MolStandardize::TautomerCatalogParams... Generating docs for compound RDKit::MolStandardize::TautomerTransform... Generating docs for compound RDKit::MolStandardize::TransformCatalogEntry... Generating docs for compound RDKit::MolStandardize::TransformCatalogParams... Generating docs for compound RDKit::MolStandardize::ValidationErrorInfo... Generating docs for compound RDKit::MolStandardize::ValidationMethod... Generating docs for compound RDKit::MolStandardize::RDKitValidation... Generating docs for compound RDKit::MolStandardize::MolVSValidations... Generating docs for compound RDKit::MolStandardize::NoAtomValidation... Generating docs for compound RDKit::MolStandardize::FragmentValidation... Generating docs for compound RDKit::MolStandardize::NeutralValidation... Generating docs for compound RDKit::MolStandardize::IsotopeValidation... Generating docs for compound RDKit::MolStandardize::MolVSValidation... Generating docs for compound RDKit::MolStandardize::AllowedAtomsValidation... Generating docs for compound RDKit::MolStandardize::DisallowedAtomsValidation... Generating docs for namespace RDKit::MolStandardize::TautomerScoringFunctions Generating docs for namespace RDKit::MorganFingerprint Generating docs for compound RDKit::MorganFingerprint::MorganAtomInvGenerator... Generating docs for compound RDKit::MorganFingerprint::MorganFeatureAtomInvGenerator... Generating docs for compound RDKit::MorganFingerprint::MorganBondInvGenerator... Generating docs for compound RDKit::MorganFingerprint::MorganArguments... Generating docs for compound RDKit::MorganFingerprint::MorganAtomEnv... Generating docs for compound RDKit::Mor/build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganFingerprints.h:157: warning: The following parameter of RDKit::MorganFingerprints::getHashedFingerprint(const ROMol &mol, unsigned int radius, unsigned int nBits=2048, std::vector< boost::uint32_t > *invariants=nullptr, const std::vector< boost::uint32_t > *fromAtoms=nullptr, bool useChirality=false, bool useBondTypes=true, bool onlyNonzeroInvariants=false, BitInfoMap *atomsSettingBits=nullptr, bool includeRedundantEnvironments=false) is not documented: parameter 'nBits' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/RDKitFPGenerator.h:76: warning: The following parameter of RDKit::RDKitFP::RDKitFPAtomEnv::getBitId(FingerprintArguments< OutputType > *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, const AdditionalOutput *AdditionalOutput, bool hashResults=false) const is not documented: parameter 'AdditionalOutput' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ReducedGraphs/ReducedGraphs.h:34: warning: The following parameter of RDKit::ReducedGraphs::generateMolExtendedReducedGraph(const ROMol &mol, std::vector< boost::dynamic_bitset<>> *atomTypes=nullptr) is not documented: parameter 'atomTypes' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/SanitizeRxn.h:126: warning: argument 'operationThatFailed' of command @param is not found in the argument list of RDKit::RxnOps::sanitizeRxn(ChemicalReaction &rxn, unsigned int &operationsThatFailed, unsigned int sanitizeOps=SANITIZE_ALL, const MolOps::AdjustQueryParameters ¶ms=DefaultRxnAdjustParams()) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/SanitizeRxn.h:156: warning: The following parameters of RDKit::RxnOps::sanitizeRxn(ChemicalReaction &rxn, unsigned int &operationsThatFailed, unsigned int sanitizeOps=SANITIZE_ALL, const MolOps::AdjustQueryParameters ¶ms=DefaultRxnAdjustParams()) are not documented: parameter 'operationsThatFailed' parameter 'params' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:89: warning: argument 'useCountSimulation' of command @param is not found in the argument list of RDKit::TopologicalTorsion::getTopologicalTorsionGenerator(const bool includeChirality=false, const uint32_t torsionAtomCount=4, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, const bool countSimulation=true, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const std::uint32_t fpSize=2048, const bool ownsAtomInvGen=false) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:109: warning: The following parameter of RDKit::TopologicalTorsion::getTopologicalTorsionGenerator(const bool includeChirality=false, const uint32_t torsionAtomCount=4, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, const bool countSimulation=true, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const std::uint32_t fpSize=2048, const bool ownsAtomInvGen=false) is not documented: parameter 'countSimulation' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:35: warning: argument 'useCountSimulation' of command @param is not found in the argument list of RDKit::TopologicalTorsion::TopologicalTorsionArguments< OutputType >::TopologicalTorsionArguments(const bool includeChirality, const uint32_t torsionAtomCount, const bool countSimulation, const std::vector< std::uint32_t > countBounds, const std::uint32_t fpSize) /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:44: warning: The following parameter of RDKit::TopologicalTorsion::TopologicalTorsionArguments::TopologicalTorsionArguments(const bool includeChirality, const uint32_t torsionAtomCount, const bool countSimulation, const std::vector< std::uint32_t > countBounds, const std::uint32_t fpSize) is not documented: parameter 'countSimulation' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:57: warning: The following parameter of RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv::getBitId(FingerprintArguments< OutputType > *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, const AdditionalOutput *AdditionalOutput, const bool hashResults=false) const is not documented: parameter 'AdditionalOutput' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/HierarchicalClusterPicker.h:80: warning: The following parameter of RDPickers::HierarchicalClusterPicker::pick(const double *distMat, unsigned int poolSize, unsigned int pickSize) const is not documented: parameter 'distMat' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/LeaderPicker.h:47: warning: argument 'firstPicks' of command @param is not found in the argument list of RDPickers::LeaderPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/LeaderPicker.h:47: warning: argument 'seed' of command @param is not found in the argument list of RDPickers::LeaderPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/LeaderPicker.h:97: warning: The following parameters of RDPickers::LeaderPicker::pick(const double *distMat, unsigned int poolSize, unsigned int pickSize, const RDKit::INT_VECT &firstPicks, double threshold, int nthreads) const are not documented: parameter 'threshold' parameter 'nthreads' /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/MaxMinPicker.h:44: warning: argument 'firstPicks' of command @param is not found in the argument list of RDPickers::MaxMinPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/MaxMinPicker.h:44: warning: argument 'seed' of command @param is not found in the argument list of RDPickers::MaxMinPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const ganFingerprint::MorganEnvGenerator... Generating docs for namespace RDKit::MorganFingerprints Generating docs for compound RDKit::MorganFingerprints::ss_matcher... Generating docs for namespace RDKit::PicklerOps Generating docs for namespace RDKit::PNGData Generating docs for namespace RDKit::QueryOps Generating docs for namespace RDKit::RDKitFP Generating docs for compound RDKit::RDKitFP::RDKitFPArguments... Generating docs for compound RDKit::RDKitFP::RDKitFPAtomInvGenerator... Generating docs for compound RDKit::RDKitFP::RDKitFPAtomEnv... Generating docs for compound RDKit::RDKitFP::RDKitFPEnvGenerator... Generating docs for namespace RDKit::RDKitFPUtils Generating docs for namespace RDKit::RDTypeTag Generating docs for namespace RDKit::RDTypeTag::detail Generating docs for compound RDKit::RDTypeTag::detail::Value... Generating docs for namespace RDKit::ReactionRunnerUtils Generating docs for namespace RDKit::ReducedGraphs Generating docs for namespace RDKit::RxnOps Generating docs for namespace RDKit::ScaffoldNetwork Generating docs for compound RDKit::ScaffoldNetwork::ScaffoldNetworkParams... Generating docs for compound RDKit::ScaffoldNetwork::NetworkEdge... Generating docs for compound RDKit::ScaffoldNetwork::ScaffoldNetwork... Generating docs for namespace RDKit::ScaffoldNetwork::detail Generating docs for namespace RDKit::SGroupParsing Generating docs for namespace RDKit::SGroupWriting Generating docs for namespace RDKit::SLNParse Generating docs for compound RDKit::SLNParse::AttribType... Generating docs for namespace RDKit::SmartsWrite Generating docs for namespace RDKit::SmilesWrite Generating docs for namespace RDKit::StructureCheck Generating docs for compound RDKit::StructureCheck::ChargeFix... Generating docs for compound RDKit::StructureCheck::Ligand... Generating docs for compound RDKit::StructureCheck::AugmentedAtom... Generating docs for compound RDKit::StructureCheck::IncEntry... Generating docs for compound RDKit::StructureCheck::PathEntry... Generating docs for compound RDKit::StructureCheck::StructCheckerOptions... Generating docs for compound RDKit::StructureCheck::StructChecker... Generating docs for compound RDKit::StructureCheck::StructCheckTautomer... Generating docs for compound RDKit::StructureCheck::Neighbourhood... Generating docs for namespace RDKit::Subgraphs Generating docs for namespace RDKit::SubstanceGroupChecks Generating docs for namespace RDKit::TopologicalTorsion Generating docs for compound RDKit::TopologicalTorsion::TopologicalTorsionArguments... Generating docs for compound RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv... Generating docs for compound RDKit::TopologicalTorsion::TopologicalTorsionEnvGenerator... Generating docs for namespace RDKit::UFF Generating docs for namespace RDKit::UFF::Tools Generating docs for compound RDKit::UFF::Tools::DefaultTorsionBondSmarts... Generating docs for namespace RDKit::Utils Generating docs for compound RDKit::Utils::LocaleSwitcher... Generating docs for namespace RDKit::Utils::detail Generating docs for namespace RDLog Generating docs for compound RDLog::BlockLogs... Generating docs for namespace RDNumeric Generating docs for compound RDNumeric::Matrix... Generating docs for compound RDNumeric::SquareMatrix... Generating docs for compound RDNumeric::SymmMatrix... Generating docs for compound RDNumeric::Vector... Generating docs for namespace RDNumeric::Alignments Generating docs for namespace RDNumeric::EigenSolvers Generating docs for namespace RDPickers Generating docs for compound RDPickers::DistPicker... Generating docs for compound RDPickers::HierarchicalClusterPicker... Generating docs for compound RDPickers::LeaderPicker... Generating docs for compound RDPickers::LeaderPickerState... Generating docs for compound RDPickers::MaxMinPicker... Generating docs for compound RDPickers::MaxMinPickInfo... Generating docs for namespace RingUtils Generating docs for namespace SmilesParseOps Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... lookup cache used 17650/65536 hits=133798 misses=20433 finished... (cd /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book; RDBASE=/build/rdkit-TKP8Bz/rdkit-202009.4 /usr/bin/make html) make[2]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book' mkdir -p _build/html/cppapi cp -r /build/rdkit-TKP8Bz/rdkit-202009.4/Code/docs/* _build/html/cppapi cp -r C++Examples _build/html/ sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v3.4.3 WARNING: html_static_path entry '_static' does not exist building [mo]: targets for 0 po files that are out of date building [html]: targets for 309 source files that are out of date updating environment: [new config] 309 added, 0 changed, 0 removed reading sources... [ 0%] BackwardsIncompatibleChanges /usr/lib/python3/dist-packages/recommonmark/parser.py:75: UserWarning: Container node skipped: type=document warn("Container node skipped: type={0}".format(mdnode.t)) reading sources... [ 0%] Cartridge reading sources... [ 0%] GettingStartedInC++ reading sources... 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[100%] source/rdkit.utils.spiral /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/index.rst:9: WARNING: toctree contains reference to nonexisting document 'Cookbook' WARNING: autodoc: failed to import module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Avalon' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Avalon.pyAvalonTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AllChem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Pairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Sheridan' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Torsions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.BRICS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.BuildFragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.AlignDepict' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.BulkTester' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.DescriptorUtilities' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.SDFToCSV' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.TemplateExpand' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemicalForceFields' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Crippen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.DSViewer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Descriptors3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.IPythonConsole' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.MolDrawing' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.SimilarityMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.aggCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.cairoCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.canvasbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.mplCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.qtCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.AtomTypes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.EState_VSA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.Fingerprinter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EnumerateHeterocycles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EnumerateStereoisomers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FastSDMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatFinderCLI' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapParser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapPoint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features.FeatDirUtilsRD' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features.ShowFeats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FilterCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.ClusterMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.DbFpSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.FingerprintMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.MolSimilarity' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.SimilarityScreener' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fraggle' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fraggle.FraggleSim' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FragmentMatcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fragments' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FunctionalGroups' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.GraphDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Graphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Lipinski' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MACCSkeys' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.FingerprintUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_orig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_sa' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey.InchiInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolStandardize.rdMolStandardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolSurf' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PandasTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PeriodicTable' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Generate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Gobbi_Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.LazyGenerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Matcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.SigFactory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.EmbedLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.ExcludedVolume' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.Pharmacophore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PropertyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.QED' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Randomize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Recap' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SATIS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SaltRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds.MurckoScaffold' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds.rdScaffoldNetwork' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ShowMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SimpleEnum' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SimpleEnum.Enumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.BuilderUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeAligner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeBuilder' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeObjects' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.testCombined' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers.DbMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers.MolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.TemplateAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.TorsionFingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.fmcs.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.inchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdAbbreviations' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdChemReactions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.Chem.rdChemicalFeatures.rst:2: WARNING: Title underline too short. rdkit.Chem.rdChemicalFeatures module ================================= WARNING: autodoc: failed to import module 'Chem.rdChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdCoordGen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDepictor' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDeprotect' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFMCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFingerprintGenerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.Chem.rdForceFieldHelpers.rst:2: WARNING: Title underline too short. rdkit.Chem.rdForceFieldHelpers module ================================= WARNING: autodoc: failed to import module 'Chem.rdForceFieldHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFreeSASA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMHFPFingerprint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMMPA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.Chem.rdMolChemicalFeatures.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolChemicalFeatures module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.Chem.rdMolDescriptors.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolDescriptors module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.Chem.rdMolInterchange.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolInterchange module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolInterchange' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolTransforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.Chem.rdPartialCharges.rst:2: WARNING: Title underline too short. rdkit.Chem.rdPartialCharges module ================================= WARNING: autodoc: failed to import module 'Chem.rdPartialCharges' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.Chem.rdRGroupDecomposition.rst:2: WARNING: Title underline too short. rdkit.Chem.rdRGroupDecomposition module ================================= WARNING: autodoc: failed to import module 'Chem.rdRGroupDecomposition' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdSLNParse' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdShapeHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdStructChecker' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.Chem.rdSubstructLibrary.rst:2: WARNING: Title underline too short. rdkit.Chem.rdSubstructLibrary module ================================= WARNING: autodoc: failed to import module 'Chem.rdSubstructLibrary' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdchem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdfiltercatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdfragcatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdinchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdmolfiles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdmolops' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdqueries' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdtrajectory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataManip' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataManip.Metric' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataManip.Metric.rdMetricMatrixCalc' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitEnsemble' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitEnsembleDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.HierarchyVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.LazySignature' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.TopNContainer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.VectCollection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.cDataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbConnection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbModule' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbReport' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbResultSet' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.StorageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DistanceGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DistanceGeometry.DistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.ForceField.rst:5: WARNING: Block quote ends without a blank line; unexpected unindent. WARNING: autodoc: failed to import module 'ForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ForceField.rdForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Geometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Geometry.rdGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.AnalyzeComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.BuildComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Butina' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.ClusterUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.ClusterVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Clustering' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Clusters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Murtagh' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Resemblance' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Standardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.AdjustComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.BayesComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.Composite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.CompositeRun' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.DataUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.FindQuantBounds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.MLData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Quantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.SplitData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Stats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Transforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.BuildQuantTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.BuildSigTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.DecTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.Forest' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.ID3' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.PruneTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.QuantTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.SigTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.Tree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.TreeUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.TreeVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.randomtest' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.CompoundDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.MoleculeDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.Parser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.EnrichPlot' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.GrowComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.BitClusterer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.BitRank' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.entropy' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.ML.InfoTheory.rdInfoTheory.rst:2: WARNING: Title underline too short. rdkit.ML.InfoTheory.rdInfoTheory module ====================================== WARNING: autodoc: failed to import module 'ML.InfoTheory.rdInfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.DistFunctions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNClassificationModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNRegressionModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MLUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MLUtils.VoteImg' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MatOps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage.PackageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage.Packager' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes.ClassificationModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.ActFuncs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.NetNode' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.Network' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.Trainers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.SLT' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.SLT.Risk' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Scoring.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ScreenComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.files' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Numerics' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Numerics.rdAlignment' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDConfig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDLogger' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDPaths' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDRandom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'SimDivFilters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'SimDivFilters.SimilarityPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'SimDivFilters.rdSimDivPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'TestRunner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Filter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Node' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.DbMolSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.DbPickleSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SDSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsMolFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesDupeFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesOutput' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.demo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Output' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Supply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Transform' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'rdBase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'six' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.cactvs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.chemdraw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.chemdraw_qax' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.chemutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.comhack' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.fileutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.listutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.spiral' from module 'rdkit'; the following exception was raised: No module named 'rdkit' looking for now-outdated files... none found pickling environment... done checking consistency... /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/data/README.md: WARNING: document isn't included in any toctree /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/modules.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... 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[100%] source/rdkit.utils.spiral /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:145: WARNING: None:any reference target not found: ./C++Examples/example1.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:167: WARNING: None:any reference target not found: ./C++Examples/example1.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:181: WARNING: None:any reference target not found: ./C++Examples/example1.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:194: WARNING: None:any reference target not found: ./C++Examples/example1.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:209: WARNING: None:any reference target not found: ./C++Examples/example2.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:233: WARNING: None:any reference target not found: ./C++Examples/example2.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:253: WARNING: None:any 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/build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:370: WARNING: None:any reference target not found: ./C++Examples/example3.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:397: WARNING: None:any reference target not found: ./C++Examples/example3.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:433: WARNING: None:any reference target not found: ./C++Examples/example4.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:462: WARNING: None:any reference target not found: ./C++Examples/example4.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:495: WARNING: None:any reference target not found: ./C++Examples/example4.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:506: WARNING: None:any reference target not found: ./C++Examples/example4.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:519: WARNING: None:any reference target not found: ./C++Examples/example4.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:530: WARNING: None:any reference target not found: ./C++Examples/example4.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:543: WARNING: None:any reference target not found: ./C++Examples/example5.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:570: WARNING: None:any reference target not found: ./C++Examples/example5.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:610: WARNING: None:any reference target not found: ./C++Examples/example6.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:619: WARNING: None:any reference target not found: ./C++Examples/example6.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:638: WARNING: None:any reference target not found: ./C++Examples/example6.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:651: WARNING: None:any reference target not found: ./C++Examples/example6.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:672: WARNING: None:any reference target not found: ./C++Examples/example7.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:700: WARNING: None:any reference target not found: ./C++Examples/example7.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:714: WARNING: None:any reference target not found: ./C++Examples/example7.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:734: WARNING: None:any reference target not found: ./C++Examples/example7.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:753: WARNING: None:any reference target not found: ./C++Examples/example7.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:769: WARNING: None:any reference target not found: ./C++Examples/example8.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:786: WARNING: None:any reference target not found: ./C++Examples/example8.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:798: WARNING: None:any reference target not found: ./C++Examples/example9.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:818: WARNING: None:any reference target not found: ../../Code/GraphMol/Bond.h /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:818: WARNING: None:any reference target not found: ./C++Examples/example9.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:856: WARNING: None:any reference target not found: ./C++Examples/example10.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:867: WARNING: None:any reference target not found: ./C++Examples/example10.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:880: WARNING: None:any reference target not found: ./C++Examples/CMakeLists.txt /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:883: WARNING: None:any reference target not found: ./C++Examples/example10.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:898: WARNING: None:any reference target not found: ./C++Examples/example10.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:970: WARNING: None:any reference target not found: ./C++Examples/example11.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1000: WARNING: None:any reference target not found: ./C++Examples/example11.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1019: WARNING: None:any reference target not found: ./C++Examples/example11.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1037: WARNING: None:any reference target not found: ./C++Examples/example11.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1093: WARNING: 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/build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1239: WARNING: None:any reference target not found: ./C++Examples/example13.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1265: WARNING: None:any reference target not found: ./C++Examples/example14.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1295: WARNING: None:any reference target not found: ./C++Examples/example14.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1316: WARNING: None:any reference target not found: ./C++Examples/example14.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1334: WARNING: None:any reference target not found: ./C++Examples/example14.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1352: WARNING: None:any reference target not found: ./C++Examples/example14.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1385: WARNING: None:any reference target not found: ./C++Examples/example15.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1410: WARNING: None:any reference target not found: ./C++Examples/example15.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1442: WARNING: None:any reference target not found: ./C++Examples/example15.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1470: WARNING: None:any reference target not found: ./C++Examples/example16.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1508: WARNING: None:any reference target not found: ./C++Examples/example16.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/Install.md:: WARNING: Pygments lexer name 'shellsession' is not known /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/Install.md:: WARNING: Pygments lexer name 'shellsession' is not known /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/Install.md:: WARNING: Pygments lexer name 'shellsession' is not known /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/Install.md:: WARNING: Pygments lexer name 'shellsession' is not known /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/Install.md:: WARNING: Pygments lexer name 'shellsession' is not known /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/Install.md:: WARNING: Pygments lexer name 'shellsession' is not known generating indices... genindex done writing additional pages... search done copying images... 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The HTML pages are in _build/html. make[2]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book' (cd /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book; RDBASE=/build/rdkit-TKP8Bz/rdkit-202009.4 /usr/bin/make latexpdf) make[2]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book' mkdir -p _build/html/cppapi cp -r /build/rdkit-TKP8Bz/rdkit-202009.4/Code/docs/* _build/html/cppapi sphinx-build -b latex -d _build/doctrees . _build/latex Running Sphinx v3.4.3 making output directory... done WARNING: html_static_path entry '_static' does not exist loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 0 added, 298 changed, 0 removed reading sources... [ 0%] index reading sources... [ 0%] source/rdkit reading sources... [ 1%] source/rdkit.Avalon reading sources... [ 1%] source/rdkit.Avalon.pyAvalonTools reading sources... [ 1%] source/rdkit.Chem reading sources... 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[100%] source/rdkit.utils.spiral /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/index.rst:9: WARNING: toctree contains reference to nonexisting document 'Cookbook' WARNING: autodoc: failed to import module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Avalon' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Avalon.pyAvalonTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AllChem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Pairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Sheridan' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Torsions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.BRICS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.BuildFragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.AlignDepict' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.BulkTester' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.DescriptorUtilities' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.SDFToCSV' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.TemplateExpand' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemicalForceFields' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Crippen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.DSViewer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Descriptors3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.IPythonConsole' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.MolDrawing' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.SimilarityMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.aggCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.cairoCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.canvasbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.mplCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.qtCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.AtomTypes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.EState_VSA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.Fingerprinter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EnumerateHeterocycles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EnumerateStereoisomers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FastSDMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatFinderCLI' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapParser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapPoint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features.FeatDirUtilsRD' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features.ShowFeats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FilterCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.ClusterMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.DbFpSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.FingerprintMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.MolSimilarity' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.SimilarityScreener' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fraggle' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fraggle.FraggleSim' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FragmentMatcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fragments' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FunctionalGroups' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.GraphDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Graphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Lipinski' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MACCSkeys' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.FingerprintUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_orig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_sa' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey.InchiInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolStandardize.rdMolStandardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolSurf' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PandasTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PeriodicTable' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Generate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Gobbi_Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.LazyGenerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Matcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.SigFactory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.EmbedLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.ExcludedVolume' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.Pharmacophore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PropertyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.QED' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Randomize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Recap' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SATIS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SaltRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds.MurckoScaffold' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds.rdScaffoldNetwork' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ShowMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SimpleEnum' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SimpleEnum.Enumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.BuilderUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeAligner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeBuilder' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeObjects' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.testCombined' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers.DbMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers.MolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.TemplateAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.TorsionFingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.fmcs.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.inchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdAbbreviations' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdChemReactions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.Chem.rdChemicalFeatures.rst:2: WARNING: Title underline too short. rdkit.Chem.rdChemicalFeatures module ================================= WARNING: autodoc: failed to import module 'Chem.rdChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdCoordGen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDepictor' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDeprotect' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFMCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFingerprintGenerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.Chem.rdForceFieldHelpers.rst:2: WARNING: Title underline too short. rdkit.Chem.rdForceFieldHelpers module ================================= WARNING: autodoc: failed to import module 'Chem.rdForceFieldHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFreeSASA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMHFPFingerprint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMMPA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.Chem.rdMolChemicalFeatures.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolChemicalFeatures module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.Chem.rdMolDescriptors.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolDescriptors module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.Chem.rdMolInterchange.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolInterchange module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolInterchange' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolTransforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.Chem.rdPartialCharges.rst:2: WARNING: Title underline too short. rdkit.Chem.rdPartialCharges module ================================= WARNING: autodoc: failed to import module 'Chem.rdPartialCharges' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.Chem.rdRGroupDecomposition.rst:2: WARNING: Title underline too short. rdkit.Chem.rdRGroupDecomposition module ================================= WARNING: autodoc: failed to import module 'Chem.rdRGroupDecomposition' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdSLNParse' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdShapeHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdStructChecker' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.Chem.rdSubstructLibrary.rst:2: WARNING: Title underline too short. rdkit.Chem.rdSubstructLibrary module ================================= WARNING: autodoc: failed to import module 'Chem.rdSubstructLibrary' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdchem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdfiltercatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdfragcatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdinchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdmolfiles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdmolops' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdqueries' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdtrajectory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataManip' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataManip.Metric' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataManip.Metric.rdMetricMatrixCalc' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitEnsemble' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitEnsembleDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.HierarchyVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.LazySignature' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.TopNContainer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.VectCollection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.cDataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbConnection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbModule' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbReport' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbResultSet' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.StorageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DistanceGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DistanceGeometry.DistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.ForceField.rst:5: WARNING: Block quote ends without a blank line; unexpected unindent. WARNING: autodoc: failed to import module 'ForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ForceField.rdForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Geometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Geometry.rdGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.AnalyzeComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.BuildComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Butina' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.ClusterUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.ClusterVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Clustering' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Clusters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Murtagh' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Resemblance' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Standardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.AdjustComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.BayesComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.Composite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.CompositeRun' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.DataUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.FindQuantBounds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.MLData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Quantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.SplitData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Stats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Transforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.BuildQuantTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.BuildSigTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.DecTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.Forest' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.ID3' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.PruneTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.QuantTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.SigTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.Tree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.TreeUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.TreeVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.randomtest' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.CompoundDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.MoleculeDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.Parser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.EnrichPlot' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.GrowComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.BitClusterer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.BitRank' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.entropy' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/rdkit.ML.InfoTheory.rdInfoTheory.rst:2: WARNING: Title underline too short. rdkit.ML.InfoTheory.rdInfoTheory module ====================================== WARNING: autodoc: failed to import module 'ML.InfoTheory.rdInfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.DistFunctions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNClassificationModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNRegressionModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MLUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MLUtils.VoteImg' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MatOps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage.PackageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage.Packager' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes.ClassificationModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.ActFuncs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.NetNode' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.Network' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.Trainers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.SLT' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.SLT.Risk' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Scoring.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ScreenComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.files' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Numerics' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Numerics.rdAlignment' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDConfig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDLogger' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDPaths' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDRandom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'SimDivFilters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'SimDivFilters.SimilarityPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'SimDivFilters.rdSimDivPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'TestRunner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Filter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Node' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.DbMolSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.DbPickleSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SDSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsMolFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesDupeFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesOutput' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.demo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Output' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Supply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Transform' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'rdBase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'six' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.cactvs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.chemdraw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.chemdraw_qax' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.chemutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.comhack' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.fileutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.listutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.spiral' from module 'rdkit'; the following exception was raised: No module named 'rdkit' looking for now-outdated files... none found pickling environment... done checking consistency... /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/data/README.md: WARNING: document isn't included in any toctree /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/source/modules.rst: WARNING: document isn't included in any toctree done processing RDKit.tex... index Overview Install GettingStartedInPython RDKit_Book Cartridge BackwardsIncompatibleChanges api-docs source/rdkit source/rdkit.Avalon source/rdkit.Avalon.pyAvalonTools source/rdkit.Chem source/rdkit.Chem.AtomPairs source/rdkit.Chem.AtomPairs.Pairs source/rdkit.Chem.AtomPairs.Sheridan source/rdkit.Chem.AtomPairs.Torsions source/rdkit.Chem.AtomPairs.Utils source/rdkit.Chem.ChemUtils source/rdkit.Chem.ChemUtils.AlignDepict source/rdkit.Chem.ChemUtils.BulkTester source/rdkit.Chem.ChemUtils.DescriptorUtilities source/rdkit.Chem.ChemUtils.SDFToCSV source/rdkit.Chem.ChemUtils.TemplateExpand source/rdkit.Chem.Draw source/rdkit.Chem.Draw.IPythonConsole source/rdkit.Chem.Draw.MolDrawing source/rdkit.Chem.Draw.SimilarityMaps source/rdkit.Chem.Draw.rdMolDraw2D source/rdkit.Chem.Draw.aggCanvas source/rdkit.Chem.Draw.cairoCanvas source/rdkit.Chem.Draw.canvasbase source/rdkit.Chem.Draw.mplCanvas source/rdkit.Chem.Draw.qtCanvas source/rdkit.Chem.EState source/rdkit.Chem.EState.AtomTypes source/rdkit.Chem.EState.EState source/rdkit.Chem.EState.EState_VSA source/rdkit.Chem.EState.Fingerprinter source/rdkit.Chem.FeatMaps source/rdkit.Chem.FeatMaps.FeatMapParser source/rdkit.Chem.FeatMaps.FeatMapPoint source/rdkit.Chem.FeatMaps.FeatMapUtils source/rdkit.Chem.FeatMaps.FeatMaps source/rdkit.Chem.Features source/rdkit.Chem.Features.FeatDirUtilsRD source/rdkit.Chem.Features.ShowFeats source/rdkit.Chem.Fingerprints source/rdkit.Chem.Fingerprints.ClusterMols source/rdkit.Chem.Fingerprints.DbFpSupplier source/rdkit.Chem.Fingerprints.FingerprintMols source/rdkit.Chem.Fingerprints.MolSimilarity source/rdkit.Chem.Fingerprints.SimilarityScreener source/rdkit.Chem.Fraggle source/rdkit.Chem.Fraggle.FraggleSim source/rdkit.Chem.MolDb source/rdkit.Chem.MolDb.FingerprintUtils source/rdkit.Chem.MolDb.Loader source/rdkit.Chem.MolDb.Loader_orig source/rdkit.Chem.MolDb.Loader_sa source/rdkit.Chem.MolKey source/rdkit.Chem.MolKey.InchiInfo source/rdkit.Chem.MolKey.MolKey source/rdkit.Chem.Pharm2D source/rdkit.Chem.Pharm2D.Generate source/rdkit.Chem.Pharm2D.Gobbi_Pharm2D source/rdkit.Chem.Pharm2D.LazyGenerator source/rdkit.Chem.Pharm2D.Matcher source/rdkit.Chem.Pharm2D.SigFactory source/rdkit.Chem.Pharm2D.Utils source/rdkit.Chem.Pharm3D source/rdkit.Chem.Pharm3D.EmbedLib source/rdkit.Chem.Pharm3D.ExcludedVolume source/rdkit.Chem.Pharm3D.Pharmacophore source/rdkit.Chem.Scaffolds source/rdkit.Chem.Scaffolds.MurckoScaffold source/rdkit.Chem.Scaffolds.rdScaffoldNetwork source/rdkit.Chem.SimpleEnum source/rdkit.Chem.SimpleEnum.Enumerator source/rdkit.Chem.Subshape source/rdkit.Chem.Subshape.BuilderUtils source/rdkit.Chem.Subshape.SubshapeAligner source/rdkit.Chem.Subshape.SubshapeBuilder source/rdkit.Chem.Subshape.SubshapeObjects source/rdkit.Chem.Subshape.testCombined source/rdkit.Chem.Suppliers source/rdkit.Chem.Suppliers.DbMolSupplier source/rdkit.Chem.Suppliers.MolSupplier source/rdkit.Chem.fmcs source/rdkit.Chem.fmcs.fmcs source/rdkit.Chem.AllChem source/rdkit.Chem.BRICS source/rdkit.Chem.BuildFragmentCatalog source/rdkit.Chem.ChemicalFeatures source/rdkit.Chem.ChemicalForceFields source/rdkit.Chem.Crippen source/rdkit.Chem.DSViewer source/rdkit.Chem.Descriptors source/rdkit.Chem.Descriptors3D source/rdkit.Chem.EnumerateHeterocycles source/rdkit.Chem.EnumerateStereoisomers source/rdkit.Chem.FastSDMolSupplier source/rdkit.Chem.FeatFinderCLI source/rdkit.Chem.FilterCatalog source/rdkit.Chem.FragmentCatalog source/rdkit.Chem.FragmentMatcher source/rdkit.Chem.Fragments source/rdkit.Chem.FunctionalGroups source/rdkit.Chem.GraphDescriptors source/rdkit.Chem.Graphs source/rdkit.Chem.Lipinski source/rdkit.Chem.MACCSkeys source/rdkit.Chem.MCS source/rdkit.Chem.MolCatalog source/rdkit.Chem.MolStandardize source/rdkit.Chem.MolStandardize.rdMolStandardize source/rdkit.Chem.MolSurf source/rdkit.Chem.PandasTools source/rdkit.Chem.PeriodicTable source/rdkit.Chem.PropertyMol source/rdkit.Chem.PyMol source/rdkit.Chem.QED source/rdkit.Chem.Randomize source/rdkit.Chem.Recap source/rdkit.Chem.ReducedGraphs source/rdkit.Chem.SATIS source/rdkit.Chem.SaltRemover source/rdkit.Chem.ShowMols source/rdkit.Chem.TemplateAlign source/rdkit.Chem.TorsionFingerprints source/rdkit.Chem.inchi source/rdkit.Chem.rdchem source/rdkit.Chem.rdDistGeom source/rdkit.Chem.rdqueries source/rdkit.Chem.rdFMCS source/rdkit.Chem.rdMolAlign source/rdkit.Chem.rdMolHash source/rdkit.Chem.rdReducedGraphs source/rdkit.Chem.rdtrajectory source/rdkit.Chem.rdMolTransforms source/rdkit.Chem.rdmolfiles source/rdkit.Chem.rdPartialCharges source/rdkit.Chem.rdMolCatalog source/rdkit.Chem.rdCoordGen source/rdkit.Chem.rdMolChemicalFeatures source/rdkit.Chem.rdMMPA source/rdkit.Chem.rdRGroupDecomposition source/rdkit.Chem.rdForceFieldHelpers source/rdkit.Chem.rdDepictor source/rdkit.Chem.rdChemicalFeatures source/rdkit.Chem.rdmolops source/rdkit.Chem.rdFreeSASA source/rdkit.Chem.rdMolInterchange source/rdkit.Chem.rdShapeHelpers source/rdkit.Chem.rdinchi source/rdkit.Chem.rdChemReactions source/rdkit.Chem.rdSubstructLibrary source/rdkit.Chem.rdfiltercatalog source/rdkit.Chem.rdfragcatalog source/rdkit.Chem.rdStructChecker source/rdkit.Chem.rdMolDescriptors source/rdkit.Chem.rdFingerprintGenerator source/rdkit.Chem.rdMHFPFingerprint source/rdkit.Chem.rdSLNParse source/rdkit.Chem.rdAbbreviations source/rdkit.Chem.rdDeprotect source/rdkit.DataManip source/rdkit.DataManip.Metric source/rdkit.DataManip.Metric.rdMetricMatrixCalc source/rdkit.DataStructs source/rdkit.DataStructs.BitEnsemble source/rdkit.DataStructs.BitEnsembleDb source/rdkit.DataStructs.BitUtils source/rdkit.DataStructs.HierarchyVis source/rdkit.DataStructs.LazySignature source/rdkit.DataStructs.TopNContainer source/rdkit.DataStructs.VectCollection source/rdkit.DataStructs.cDataStructs source/rdkit.Dbase source/rdkit.Dbase.DbConnection source/rdkit.Dbase.DbInfo source/rdkit.Dbase.DbModule source/rdkit.Dbase.DbReport source/rdkit.Dbase.DbResultSet source/rdkit.Dbase.DbUtils source/rdkit.Dbase.StorageUtils source/rdkit.DistanceGeometry source/rdkit.DistanceGeometry.DistGeom source/rdkit.ForceField source/rdkit.ForceField.rdForceField source/rdkit.Geometry source/rdkit.Geometry.rdGeometry source/rdkit.ML source/rdkit.ML.Cluster source/rdkit.ML.Cluster.Butina source/rdkit.ML.Cluster.ClusterUtils source/rdkit.ML.Cluster.ClusterVis source/rdkit.ML.Cluster.Clusters source/rdkit.ML.Cluster.Murtagh source/rdkit.ML.Cluster.Resemblance source/rdkit.ML.Cluster.Standardize source/rdkit.ML.Cluster.Clustering source/rdkit.ML.Composite source/rdkit.ML.Composite.AdjustComposite source/rdkit.ML.Composite.BayesComposite source/rdkit.ML.Composite.Composite source/rdkit.ML.Data source/rdkit.ML.Data.DataUtils source/rdkit.ML.Data.FindQuantBounds source/rdkit.ML.Data.MLData source/rdkit.ML.Data.Quantize source/rdkit.ML.Data.SplitData source/rdkit.ML.Data.Stats source/rdkit.ML.Data.Transforms source/rdkit.ML.DecTree source/rdkit.ML.DecTree.BuildQuantTree source/rdkit.ML.DecTree.BuildSigTree source/rdkit.ML.DecTree.CrossValidate source/rdkit.ML.DecTree.DecTree source/rdkit.ML.DecTree.Forest source/rdkit.ML.DecTree.ID3 source/rdkit.ML.DecTree.PruneTree source/rdkit.ML.DecTree.QuantTree source/rdkit.ML.DecTree.SigTree source/rdkit.ML.DecTree.Tree source/rdkit.ML.DecTree.TreeUtils source/rdkit.ML.DecTree.TreeVis source/rdkit.ML.DecTree.randomtest source/rdkit.ML.Descriptors source/rdkit.ML.Descriptors.CompoundDescriptors source/rdkit.ML.Descriptors.Descriptors source/rdkit.ML.Descriptors.MoleculeDescriptors source/rdkit.ML.Descriptors.Parser source/rdkit.ML.InfoTheory source/rdkit.ML.InfoTheory.BitClusterer source/rdkit.ML.InfoTheory.BitRank source/rdkit.ML.InfoTheory.entropy source/rdkit.ML.InfoTheory.rdInfoTheory source/rdkit.ML.KNN source/rdkit.ML.KNN.CrossValidate source/rdkit.ML.KNN.DistFunctions source/rdkit.ML.KNN.KNNClassificationModel source/rdkit.ML.KNN.KNNModel source/rdkit.ML.KNN.KNNRegressionModel source/rdkit.ML.MLUtils source/rdkit.ML.MLUtils.VoteImg source/rdkit.ML.ModelPackage source/rdkit.ML.ModelPackage.PackageUtils source/rdkit.ML.ModelPackage.Packager source/rdkit.ML.NaiveBayes source/rdkit.ML.NaiveBayes.ClassificationModel source/rdkit.ML.NaiveBayes.CrossValidate source/rdkit.ML.Neural source/rdkit.ML.Neural.ActFuncs source/rdkit.ML.Neural.CrossValidate source/rdkit.ML.Neural.NetNode source/rdkit.ML.Neural.Network source/rdkit.ML.Neural.Trainers source/rdkit.ML.SLT source/rdkit.ML.SLT.Risk source/rdkit.ML.Scoring source/rdkit.ML.Scoring.Scoring source/rdkit.ML.AnalyzeComposite source/rdkit.ML.BuildComposite source/rdkit.ML.CompositeRun source/rdkit.ML.EnrichPlot source/rdkit.ML.GrowComposite source/rdkit.ML.MatOps source/rdkit.ML.ScreenComposite source/rdkit.ML.files source/rdkit.Numerics source/rdkit.Numerics.rdAlignment source/rdkit.SimDivFilters source/rdkit.SimDivFilters.SimilarityPickers source/rdkit.SimDivFilters.rdSimDivPickers source/rdkit.VLib source/rdkit.VLib.NodeLib source/rdkit.VLib.NodeLib.DbMolSupply source/rdkit.VLib.NodeLib.DbPickleSupplier source/rdkit.VLib.NodeLib.SDSupply source/rdkit.VLib.NodeLib.SmartsMolFilter source/rdkit.VLib.NodeLib.SmartsRemover source/rdkit.VLib.NodeLib.SmilesDupeFilter source/rdkit.VLib.NodeLib.SmilesOutput source/rdkit.VLib.NodeLib.SmilesSupply source/rdkit.VLib.NodeLib.demo source/rdkit.VLib.Filter source/rdkit.VLib.Node source/rdkit.VLib.Output source/rdkit.VLib.Supply source/rdkit.VLib.Transform source/rdkit.utils source/rdkit.utils.cactvs source/rdkit.utils.chemdraw source/rdkit.utils.chemdraw_qax source/rdkit.utils.chemutils source/rdkit.utils.comhack source/rdkit.utils.fileutils source/rdkit.utils.listutils source/rdkit.utils.spiral source/rdkit.rdBase source/rdkit.RDConfig source/rdkit.RDLogger source/rdkit.RDPaths source/rdkit.RDRandom source/rdkit.TestRunner source/rdkit.six GettingStartedInC++ resolving references... /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:145: WARNING: None:any reference target not found: ./C++Examples/example1.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:167: WARNING: None:any reference target not found: ./C++Examples/example1.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:181: WARNING: None:any reference target not found: ./C++Examples/example1.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:194: WARNING: None:any reference target not found: ./C++Examples/example1.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:209: WARNING: None:any reference target not found: ./C++Examples/example2.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:233: WARNING: None:any reference target not found: ./C++Examples/example2.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:253: WARNING: None:any reference target not found: ./C++Examples/example2.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:270: WARNING: None:any reference target not found: ./C++Examples/example2.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:294: WARNING: None:any reference target not found: ./C++Examples/example2.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:308: WARNING: None:any reference target not found: ./C++Examples/example3.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:321: WARNING: None:any reference target not found: ./C++Examples/example3.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:330: WARNING: None:any reference target not found: ./C++Examples/example3.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:349: WARNING: None:any reference target not found: ./C++Examples/example3.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:370: WARNING: None:any reference target not found: ./C++Examples/example3.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:397: WARNING: None:any reference target not found: ./C++Examples/example3.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:433: WARNING: None:any reference target not found: ./C++Examples/example4.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:462: WARNING: None:any reference target not found: ./C++Examples/example4.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:495: WARNING: None:any reference target not found: ./C++Examples/example4.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:506: WARNING: None:any reference target not found: ./C++Examples/example4.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:519: WARNING: None:any reference target not found: ./C++Examples/example4.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:530: WARNING: None:any reference target not found: ./C++Examples/example4.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:543: WARNING: None:any reference target not found: ./C++Examples/example5.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:570: WARNING: None:any reference target not found: ./C++Examples/example5.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:610: WARNING: None:any reference target not found: ./C++Examples/example6.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:619: WARNING: None:any reference target not found: ./C++Examples/example6.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:638: WARNING: None:any reference target not found: ./C++Examples/example6.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:651: WARNING: None:any reference target not found: ./C++Examples/example6.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:672: WARNING: None:any reference target not found: ./C++Examples/example7.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:700: WARNING: None:any reference target not found: ./C++Examples/example7.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:714: WARNING: None:any reference target not found: ./C++Examples/example7.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:734: WARNING: None:any reference target not found: ./C++Examples/example7.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:753: WARNING: None:any reference target not found: ./C++Examples/example7.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:769: WARNING: None:any reference target not found: ./C++Examples/example8.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:786: WARNING: None:any reference target not found: ./C++Examples/example8.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:798: WARNING: None:any reference target not found: ./C++Examples/example9.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:818: WARNING: None:any reference target not found: ../../Code/GraphMol/Bond.h /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:818: WARNING: None:any reference target not found: ./C++Examples/example9.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:856: WARNING: None:any reference target not found: ./C++Examples/example10.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:867: WARNING: None:any reference target not found: ./C++Examples/example10.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:880: WARNING: None:any reference target not found: ./C++Examples/CMakeLists.txt /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:883: WARNING: None:any reference target not found: ./C++Examples/example10.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:898: WARNING: None:any reference target not found: ./C++Examples/example10.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:970: WARNING: None:any reference target not found: ./C++Examples/example11.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1000: WARNING: None:any reference target not found: ./C++Examples/example11.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1019: WARNING: None:any reference target not found: ./C++Examples/example11.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1037: WARNING: None:any reference target not found: ./C++Examples/example11.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1093: WARNING: None:any reference target not found: ./C++Examples/example12.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1107: WARNING: None:any reference target not found: ./C++Examples/example12.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1155: WARNING: None:any reference target not found: ./C++Examples/example13.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1179: WARNING: None:any reference target not found: ./C++Examples/example13.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1190: WARNING: None:any reference target not found: ./C++Examples/example13.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1208: WARNING: None:any reference target not found: ./C++Examples/example17.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1233: WARNING: None:any reference target not found: ./C++Examples/example17.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1239: WARNING: None:any reference target not found: ./C++Examples/example13.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1265: WARNING: None:any reference target not found: ./C++Examples/example14.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1295: WARNING: None:any reference target not found: ./C++Examples/example14.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1316: WARNING: None:any reference target not found: ./C++Examples/example14.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1334: WARNING: None:any reference target not found: ./C++Examples/example14.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1352: WARNING: None:any reference target not found: ./C++Examples/example14.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1385: WARNING: None:any reference target not found: ./C++Examples/example15.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1410: WARNING: None:any reference target not found: ./C++Examples/example15.cpp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:1442: WARNING: None:any reference target not found: ./C++Examples/example15.cpp 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(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] [1] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Underfull \hbox (badness 10000) in paragraph at lines 123--124 []\T1/ptm/m/n/10 Cheminformatics nodes for KN-IME (dis-tributed from the KN-IME com-mu-nity site: [1] LaTeX Warning: Hyper reference `Overview:footnote1' on page 2 undefined on inpu t line 217. [2] [3] [4] Chapter 2. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [5] [6] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [7] [8] [9] [10] Underfull \hbox (badness 10000) in paragraph at lines 746--747 []\T1/ptm/m/n/10 You can en-able sup-port for the Avalon toolkit by adding the ar-gu-ment [11] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 815. 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[81 <./picture_9.png (PNG copy)>] [82 <./picture_8.png> <./picture_7.png (PNG c opy)>] [83 <./picture_10.png> <./picture_12.png>] [84 <./picture_11.png>] [85] [86] Overfull \vbox (5.17178pt too high) detected at line 5258 [87] [88] [89] Underfull \hbox (badness 10000) in paragraph at lines 5644--5646 []\T1/ptm/m/n/10 metals, [90] [91 <./parastereo_2.png> <./parastereo_1.png>] [92 <./potential_stereo_dou ble_bond1.png> <./potential_stereo_double_bond2.png> <./potential_stereo_double _bond3.png>] [93] [94] [95] [96] [97] [98] [99] LaTeX Warning: Hyper reference `RDKit_Book:ph4-figure' on page 100 undefined on input line 6353. 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[107] Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/phv/m/n/10 Mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- [108] [109 <./enhanced_stereo_and1_and2_base.png> <./enhanced_stereo_and1_and2_ expand.png> <./enhanced_stereo_and1_cis_base.png> <./enhanced_stereo_and1_cis_e xpand.png> <./enhanced_stereo_and1_trans_base.png> <./enhanced_stereo_and1_tran s_expand.png> <./enhanced_stereo_or1_or2_base.png> <./enhanced_stereo_or1_cis_b ase.png> <./enhanced_stereo_or1_trans_base.png> <./enhanced_stereo_abs_and_base .png> <./enhanced_stereo_abs_and_expand.png> <./enhanced_stereo_abs_or_base.png >] Underfull \hbox (badness 7558) in paragraph at lines 7102--7104 []\T1/ptm/m/n/10 It is pos-si-ble to enu-mer-ate the el-e-ments of a \T1/pcr/m/ n/10 StereoGroup \T1/ptm/m/n/10 us-ing the func-tion \T1/pcr/m/n/10 rdkit.Chem. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Underfull \hbox (badness 10000) in paragraph at lines 7116--7117 []\T1/ptm/m/n/10 Reactions also pre-serve \T1/pcr/m/n/10 StereoGroup\TS1/cmtt/m /n/10 ``\T1/pcr/m/n/10 s. Product atoms are included in the Underfull \hbox (badness 10000) in paragraph at lines 7159--7161 [] Underfull \hbox (badness 10000) in paragraph at lines 7270--7272 [] [110] [111 <./EnhancedStereoSSS_molA.png> <./EnhancedStereoSSS_molB.png> <./Enh ancedStereoSSS_molC.png> <./EnhancedStereoSSS_molD.png> <./EnhancedStereoSSS_mo lE.png> <./EnhancedStereoSSS_molF.png> <./EnhancedStereoSSS_molG.png>] [112] [113] [114] Chapter 5. 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[133] Underfull \hbox (badness 10000) in paragraph at lines 8641--8644 \T1/ptm/m/n/10 Uncharger::uncharge() will now neu-tral-ize \T1/pcr/m/n/10 [Cl,B r,I][O-], [Cl,Br,I](=O)[O-], [Cl,Br, Underfull \hbox (badness 10000) in paragraph at lines 8641--8644 \T1/pcr/m/n/10 I](=O)(=O)[O-], [Cl,Br,I](=O)(=O)(=O)[O-], [O-]N=N[O-], [N,P](=O )[O-], Underfull \hbox (badness 10000) in paragraph at lines 8641--8644 \T1/pcr/m/n/10 [N+](=O)([O-])[O-], P(=O)([O-])[O-], P(=O)([O-])([O-])[O-], S([O -])[O-], [134] [135] [136] Chapter 7. [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] Chapter 8. [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 10677. 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[183] (./RDKit.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tctt1000 mkdir: cannot create directory ‘././nonexistent’: Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tctt1000 This is METAFONT, Version 2.7182818 (TeX Live 2020/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tctt1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tctt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) Font metrics written on tctt1000.tfm. 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) {/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8 r.enc} kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1000 mkdir: cannot create directory ‘././nonexistent’: Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1000 This is METAFONT, Version 2.7182818 (TeX Live 2020/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06943pt) Font metrics written on tcrm1000.tfm. 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Underfull \hbox (badness 10000) in paragraph at lines 123--124 []\T1/ptm/m/n/10 Cheminformatics nodes for KN-IME (dis-tributed from the KN-IME com-mu-nity site: [1] LaTeX Warning: Hyper reference `Overview:footnote1' on page 2 undefined on inpu t line 217. [2] [3] [4] Chapter 2. [5] [6] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [7] [8] [9] [10] Underfull \hbox (badness 10000) in paragraph at lines 746--747 []\T1/ptm/m/n/10 You can en-able sup-port for the Avalon toolkit by adding the ar-gu-ment [11] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 815. (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) Underfull \hbox (badness 10000) in paragraph at lines 844--845 []\T1/ptm/m/n/10 Add \T1/pcr/m/n/10 #define BOOST_PYTHON_NO_PY_SIGNATURES \T1/p tm/m/n/10 at the top of \T1/pcr/m/n/10 Code/GraphMol/Wrap/ [12] [13] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 951. Underfull \hbox (badness 10000) in paragraph at lines 951--952 \T1/pcr/m/n/10 installed to \T1/ptm/m/n/10 C:\boost\T1/pcr/m/n/10 , and that yo u will build the RDKit from a directory named Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 969. [14] Underfull \hbox (badness 10000) in paragraph at lines 991--992 []\T1/ptm/m/n/10 Run cmake. Here's an ex-am-ple ba-sic com-mand line for 64bit win-dows that will Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/ptm/m/n/10 down-load the InChI and Avalon toolkit sources from the InChI Tr ust and Source-Forge Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/ptm/m/n/10 repos-i-to-ries, re-spec-tively, and build the Post-greSQL car-t ridge for the in-stalled ver-sion Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/ptm/m/n/10 of Post-greSQL:\T1/pcr/m/n/10 cmake -DRDK_BUILD_PYTHON_WRAPPERS= ON -DBOOST_ROOT=C:/ Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/pcr/m/n/10 boost -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/pcr/m/n/10 -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\Postgre SQL\9.5" Underfull \hbox (badness 10000) in paragraph at lines 1000--1001 []\T1/pcr/m/n/10 "C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresq l-9.5" Underfull \hbox (badness 10000) in paragraph at lines 1006--1007 []\T1/pcr/m/n/10 "C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresq l-9.5" [15] [16] Chapter 3. [17] Underfull \hbox (badness 10000) in paragraph at lines 1102--1103 []\T1/ptm/m/n/10 displays a mes-sage like: \T1/pcr/m/n/10 [12:18:01] Explicit v alence for atom # 1 O greater than [18] [19] [20] [21] Overfull \vbox (1.28346pt too high) detected at line 1420 [22] [23] [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 1652--1654 []\T1/ptm/m/n/10 Another op-tion for Com-pute2DCoords al-lows you to gen-er-ate 2D de-pic-tions for molecules that Underfull \hbox (badness 7649) in paragraph at lines 1652--1654 \T1/ptm/m/n/10 closely mimic 3D con-for-ma-tions. This is avail-able us-ing the func-tion \T1/pcr/m/n/10 rdkit.Chem.AllChem. [26 <./picture_1.png (PNG copy)> <./picture_0.png (PNG copy)> <./picture_3.png (PNG copy)>] Underfull \hbox (badness 10000) in paragraph at lines 1672--1677 []\T1/ptm/m/n/10 More fine-grained con-trol can be ob-tained us-ing the core fu nc-tion \T1/pcr/m/n/10 rdkit.Chem.rdDepictor. [27 <./picture_2.png> <./picture_4.png>] [28] [29] [30 <./cdk2_mol1.png> <./cdk 2_mol2.png>] [31 <./cdk2_molgrid.png (PNG copy)>] Underfull \vbox (badness 2707) detected at line 1972 [32 <./cdk2_molgrid_aligned.png (PNG copy)>] [33 <./atom_highlights_1.png>] [34 <./atom_highlights_2.png> <./atom_highlights_3.png>] [35 <./atom_annotation _1.png>] [36 <./atom_labels_1.png>] [37 <./atom_labels_2.png>] [38 <./atom_labe ls_3.png>] [39 <./mol_metadata1.png>] [40] [41] [42] [43 <./substruct_search_pa rameters1.png>] [44] [45] [46] [47] [48] [49] [50] [51] [52 <./mfp2_bit872.png> <./rdk_bit1553.png>] [53 <./rdk_bit1553_2.png>] [54] [55 <./similarity_map_fp1 .png>] [56 <./similarity_map_fp2.png>] [57 <./similarity_map_fp3.png>] [58] [59 <./similarity_map_charges.png>] [60 <./similarity_map_crippen.png>] [61] Overfull \hbox (59.44438pt too wide) in paragraph at lines 3309--3309 []\T1/pcr/m/n/9 [cH:5]1[cH:6][c:7]2[cH:8][n:9][cH:10][cH:11][c:12]2[c:3]([cH:4] 1)[C:2](=[O:1])[N:13]=[N+:14]=[N- [62 <./reaction1.png>] [63 <./reaction1_highlight.png>] [64] [65] [66] [67] [68] [69] [70] Underfull \hbox (badness 6792) in paragraph at lines 3922--3925 []\T1/ptm/m/n/10 Or we can use the bit rank-ing func-tion-al-ity from the \T1/p cr/m/n/10 rdkit.ML.InfoTheory.rdInfoTheory. [71] [72] [73] [74 <./picture_6.png>] [75] Overfull \hbox (520.56647pt too wide) in alignment at lines 4193--4196 [] [] [] Overfull \hbox (520.56647pt too wide) in alignment at lines 4196--4202 [] [] [] Overfull \hbox (520.56647pt too wide) in alignment at lines 4202--4206 [] [] [] Overfull \hbox (520.56647pt too wide) in alignment at lines 4206--4208 [] [] [] Overfull \hbox (520.56647pt too wide) in alignment at lines 4208--4359 [] [] [] Overfull \hbox (520.56647pt too wide) in alignment at lines 4359--4509 [] [] [] Overfull \hbox (520.56647pt too wide) in alignment at lines 4509--4518 [] [] [] [76] Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 De-scrip- Overfull \hbox (19.3687pt too wide) in paragraph at lines 4661--4661 \T1/ptm/m/n/10 tor/Descriptor Overfull \hbox (3.88354pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 Lan- Overfull \hbox (8.88354pt too wide) in paragraph at lines 4661--4661 \T1/ptm/m/n/10 guage| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 \T1/ptm/m/n/10 best fit Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 PMI1, Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 \T1/ptm/m/n/10 PMI2, Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 NPR1, Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 Ra-dius Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 In-er-tial Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 \T1/ptm/m/n/10 shape Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 Ec-cen- Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 As- Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 Sphe-roc- Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 Au-to- Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 GET- Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| [77] Underfull \hbox (badness 10000) in paragraph at lines 4750--4750 []\T1/ptm/m/n/10 Fin-ger-print Underfull \hbox (badness 10000) in paragraph at lines 4750--4750 []\T1/ptm/m/n/10 Lan- Overfull \hbox (2.77637pt too wide) in paragraph at lines 4750--4750 \T1/ptm/m/n/10 guage| Underfull \hbox (badness 10000) in paragraph at lines 4750--4750 []\T1/ptm/m/n/10 Topo-log-i-cal Underfull \hbox (badness 10000) in paragraph at lines 4750--4750 []\T1/ptm/m/n/10 Mor- Underfull \hbox (badness 10000) in paragraph at lines 4750--4750 []\T1/ptm/m/n/10 2D Phar-ma- Underfull \hbox (badness 10000) in paragraph at lines 4750--4750 []\T1/ptm/m/n/10 MHFP and [78] Overfull \hbox (0.97221pt too wide) in paragraph at lines 4800--4800 []\T1/ptm/m/n/10 Fea- Overfull \hbox (8.75237pt too wide) in paragraph at lines 4800--4800 []\T1/ptm/m/n/10 Donor| Underfull \hbox (badness 10000) in paragraph at lines 4800--4800 []\T1/ptm/m/n/10 Ac- Underfull \hbox (badness 10000) in paragraph at lines 4800--4800 []\T1/pcr/m/n/10 [$([O,S;H1;v2;!$(*-*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;-]),$( [N;v3;! Overfull \hbox (2.08232pt too wide) in paragraph at lines 4800--4800 []\T1/ptm/m/n/10 Aro- Overfull \hbox (5.422pt too wide) in paragraph at lines 4800--4800 \T1/ptm/m/n/10 matic| Overfull \hbox (5.9722pt too wide) in paragraph at lines 4800--4800 []\T1/ptm/m/n/10 Halo- Underfull \hbox (badness 10000) in paragraph at lines 4800--4800 []\T1/ptm/m/n/10 Ba- Underfull \hbox (badness 10000) in paragraph at lines 4800--4800 []\T1/pcr/m/n/10 [#7;+,$([N;H2&+0][$([C,a]);!$([C,a](=O))]),$([N;H1&+0]([$([C,a ]);! Underfull \hbox (badness 10000) in paragraph at lines 4800--4800 \T1/pcr/m/n/10 $([C,a](=O))])[$([C,a]);!$([C,a](=O))]),$([N;H0&+0]([C;!$(C(=O)) ])([C;! Overfull \hbox (9.86208pt too wide) in paragraph at lines 4800--4800 []\T1/ptm/m/n/10 Acidic| [79 <./picture_5.png (PNG copy)>] [80] Chapter 4. [81 <./picture_9.png (PNG copy)>] [82 <./picture_8.png> <./picture_7.png (PNG c opy)>] [83 <./picture_10.png> <./picture_12.png>] [84 <./picture_11.png>] [85] [86] Overfull \vbox (5.17178pt too high) detected at line 5258 [87] [88] [89] Underfull \hbox (badness 10000) in paragraph at lines 5644--5646 []\T1/ptm/m/n/10 metals, [90] [91 <./parastereo_2.png> <./parastereo_1.png>] [92 <./potential_stereo_dou ble_bond1.png> <./potential_stereo_double_bond2.png> <./potential_stereo_double _bond3.png>] [93] [94] [95] [96] [97] [98] [99] [100] [101 <./picture_10.jpg>] Overfull \vbox (2.72571pt too high) detected at line 6557 [102] [103] Underfull \hbox (badness 10000) in paragraph at lines 6787--6787 []\T1/ptm/m/n/10 _Chi-ral-i-ty-Pos-si- Underfull \hbox (badness 10000) in paragraph at lines 6787--6787 []\T1/ptm/m/n/10 _Re-ac-tion-De- Underfull \hbox (badness 10000) in paragraph at lines 6787--6787 []\T1/ptm/m/n/10 mo-lAtomMap- Underfull \hbox (badness 10000) in paragraph at lines 6787--6787 []\T1/ptm/m/n/10 molFileIn-ver- Underfull \hbox (badness 10000) in paragraph at lines 6787--6787 []\T1/ptm/m/n/10 mol-Rxn-Com-po- [104] [105] Underfull \hbox (badness 10000) in paragraph at lines 6926--6930 []\T1/ptm/m/n/10 By de-fault the \T1/pcr/m/n/10 rdkit.Chem.rdmolfiles.SDMolSupp lier \T1/ptm/m/n/10 and \T1/pcr/m/n/10 rdkit.Chem.rdmolfiles. Underfull \hbox (badness 6559) in paragraph at lines 6926--6930 \T1/pcr/m/n/10 ForwardSDMolSupplier \T1/ptm/m/n/10 classes (\T1/pcr/m/n/10 RDKi t::SDMolSupplier \T1/ptm/m/n/10 and \T1/pcr/m/n/10 RDKit::ForwardMolSupplier [106] Underfull \hbox (badness 10000) in paragraph at lines 6975--6978 []\T1/ptm/m/n/10 If you have atom prop-er-ties that you would like to have writ -ten to SDF files, you can Underfull \hbox (badness 10000) in paragraph at lines 6975--6978 \T1/ptm/m/n/10 use the func-tions \T1/pcr/m/n/10 rdkit.Chem.rdmolfiles.CreateAt omStringPropertyList()\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6975--6978 \T1/pcr/m/n/10 rdkit.Chem.rdmolfiles.CreateAtomIntPropertyList()\T1/ptm/m/n/10 , \T1/pcr/m/n/10 rdkit.Chem. Underfull \hbox (badness 10000) in paragraph at lines 6975--6978 \T1/pcr/m/n/10 rdmolfiles.CreateAtomDoublePropertyList()\T1/ptm/m/n/10 , or \T1 /pcr/m/n/10 rdkit.Chem.rdmolfiles. [107] Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/phv/m/n/10 Mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- [108] [109 <./enhanced_stereo_and1_and2_base.png> <./enhanced_stereo_and1_and2_ expand.png> <./enhanced_stereo_and1_cis_base.png> <./enhanced_stereo_and1_cis_e xpand.png> <./enhanced_stereo_and1_trans_base.png> <./enhanced_stereo_and1_tran s_expand.png> <./enhanced_stereo_or1_or2_base.png> <./enhanced_stereo_or1_cis_b ase.png> <./enhanced_stereo_or1_trans_base.png> <./enhanced_stereo_abs_and_base .png> <./enhanced_stereo_abs_and_expand.png> <./enhanced_stereo_abs_or_base.png >] Underfull \hbox (badness 7558) in paragraph at lines 7102--7104 []\T1/ptm/m/n/10 It is pos-si-ble to enu-mer-ate the el-e-ments of a \T1/pcr/m/ n/10 StereoGroup \T1/ptm/m/n/10 us-ing the func-tion \T1/pcr/m/n/10 rdkit.Chem. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Underfull \hbox (badness 10000) in paragraph at lines 7116--7117 []\T1/ptm/m/n/10 Reactions also pre-serve \T1/pcr/m/n/10 StereoGroup\TS1/cmtt/m /n/10 ``\T1/pcr/m/n/10 s. Product atoms are included in the Underfull \hbox (badness 10000) in paragraph at lines 7159--7161 [] Underfull \hbox (badness 10000) in paragraph at lines 7270--7272 [] [110] [111 <./EnhancedStereoSSS_molA.png> <./EnhancedStereoSSS_molB.png> <./Enh ancedStereoSSS_molC.png> <./EnhancedStereoSSS_molD.png> <./EnhancedStereoSSS_mo lE.png> <./EnhancedStereoSSS_molF.png> <./EnhancedStereoSSS_molG.png>] [112] [113] [114] Chapter 5. [115] [116] [117] [118] Overfull \hbox (1096.24321pt too wide) in paragraph at lines 7756--7756 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][ ]2[]CCCN2C([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O) [C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ]([C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)CC)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CO)NC([]=[]O)[C[]\T1/pcr /b/n/9 @H[]\T1/pcr/m/n/9 ](C)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ]([C []\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)O)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T 1/pcr/m/n/9 ][]2[]CSSC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](NC1[]=[]O)C([]=[]O) N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1cnc[nH][]1[])C([]=[]O)N[C[]\T1/p cr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1 /pcr/m/n/9 ](CCCNC([]=[]N)N)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1c[nH]c3ccccc13)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCNC( []=[]N)N)C([]=[]O)N2| Overfull \hbox (167.44426pt too wide) in paragraph at lines 7758--7758 []\T1/pcr/m/n/9 CN1C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCNC([]=[]N) N)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2ccc(O)cc2)NC([]=[]O)[ C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O)[C[]\T1/pcr/b/n/9 @ H[]\T1/pcr/m/n/9 ](Cc2ccc3ccccc3c2)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr /m/n/9 ][]1[]CC([]=[]O)O| Overfull \hbox (113.44432pt too wide) in paragraph at lines 7759--7759 []\T1/pcr/m/n/9 NCCCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](NC([]=[]O)[C[]\T1/pc r/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccc(OP([]=[]O)(O)O)cc1)NC([]=[]O)Cc1ccccc1)C([]= []O)N1CCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]C([]=[]O)N[C[]@[][]\T1/pcr/b /n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C(N)[]=[]O| Overfull \hbox (675.04369pt too wide) in paragraph at lines 7760--7760 []\T1/pcr/m/n/9 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Underfull \hbox (badness 10000) in paragraph at lines 123--124 []\T1/ptm/m/n/10 Cheminformatics nodes for KN-IME (dis-tributed from the KN-IME com-mu-nity site: [1] LaTeX Warning: Hyper reference `Overview:footnote1' on page 2 undefined on inpu t line 217. [2] [3] [4] Chapter 2. [5] [6] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [7] [8] [9] [10] Underfull \hbox (badness 10000) in paragraph at lines 746--747 []\T1/ptm/m/n/10 You can en-able sup-port for the Avalon toolkit by adding the ar-gu-ment [11] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 815. 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Here's an ex-am-ple ba-sic com-mand line for 64bit win-dows that will Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/ptm/m/n/10 down-load the InChI and Avalon toolkit sources from the InChI Tr ust and Source-Forge Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/ptm/m/n/10 repos-i-to-ries, re-spec-tively, and build the Post-greSQL car-t ridge for the in-stalled ver-sion Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/ptm/m/n/10 of Post-greSQL:\T1/pcr/m/n/10 cmake -DRDK_BUILD_PYTHON_WRAPPERS= ON -DBOOST_ROOT=C:/ Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/pcr/m/n/10 boost -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/pcr/m/n/10 -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\Postgre SQL\9.5" Underfull \hbox (badness 10000) in paragraph at lines 1000--1001 []\T1/pcr/m/n/10 "C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresq l-9.5" Underfull \hbox (badness 10000) in paragraph at lines 1006--1007 []\T1/pcr/m/n/10 "C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresq l-9.5" [15] [16] Chapter 3. [17] Underfull \hbox (badness 10000) in paragraph at lines 1102--1103 []\T1/ptm/m/n/10 displays a mes-sage like: \T1/pcr/m/n/10 [12:18:01] Explicit v alence for atom # 1 O greater than [18] [19] [20] [21] Overfull \vbox (1.28346pt too high) detected at line 1420 [22] [23] [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 1652--1654 []\T1/ptm/m/n/10 Another op-tion for Com-pute2DCoords al-lows you to gen-er-ate 2D de-pic-tions for molecules that Underfull \hbox (badness 7649) in paragraph at lines 1652--1654 \T1/ptm/m/n/10 closely mimic 3D con-for-ma-tions. This is avail-able us-ing the func-tion \T1/pcr/m/n/10 rdkit.Chem.AllChem. [26 <./picture_1.png (PNG copy)> <./picture_0.png (PNG copy)> <./picture_3.png (PNG copy)>] Underfull \hbox (badness 10000) in paragraph at lines 1672--1677 []\T1/ptm/m/n/10 More fine-grained con-trol can be ob-tained us-ing the core fu nc-tion \T1/pcr/m/n/10 rdkit.Chem.rdDepictor. 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[107] Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/phv/m/n/10 Mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- [108] [109 <./enhanced_stereo_and1_and2_base.png> <./enhanced_stereo_and1_and2_ expand.png> <./enhanced_stereo_and1_cis_base.png> <./enhanced_stereo_and1_cis_e xpand.png> <./enhanced_stereo_and1_trans_base.png> <./enhanced_stereo_and1_tran s_expand.png> <./enhanced_stereo_or1_or2_base.png> <./enhanced_stereo_or1_cis_b ase.png> <./enhanced_stereo_or1_trans_base.png> <./enhanced_stereo_abs_and_base .png> <./enhanced_stereo_abs_and_expand.png> <./enhanced_stereo_abs_or_base.png >] Underfull \hbox (badness 7558) in paragraph at lines 7102--7104 []\T1/ptm/m/n/10 It is pos-si-ble to enu-mer-ate the el-e-ments of a \T1/pcr/m/ n/10 StereoGroup \T1/ptm/m/n/10 us-ing the func-tion \T1/pcr/m/n/10 rdkit.Chem. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Underfull \hbox (badness 10000) in paragraph at lines 7116--7117 []\T1/ptm/m/n/10 Reactions also pre-serve \T1/pcr/m/n/10 StereoGroup\TS1/cmtt/m /n/10 ``\T1/pcr/m/n/10 s. Product atoms are included in the Underfull \hbox (badness 10000) in paragraph at lines 7159--7161 [] Underfull \hbox (badness 10000) in paragraph at lines 7270--7272 [] [110] [111 <./EnhancedStereoSSS_molA.png> <./EnhancedStereoSSS_molB.png> <./Enh ancedStereoSSS_molC.png> <./EnhancedStereoSSS_molD.png> <./EnhancedStereoSSS_mo lE.png> <./EnhancedStereoSSS_molF.png> <./EnhancedStereoSSS_molG.png>] [112] [113] [114] Chapter 5. [115] [116] [117] [118] Overfull \hbox (1096.24321pt too wide) in paragraph at lines 7756--7756 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][ ]2[]CCCN2C([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O) [C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ]([C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)CC)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CO)NC([]=[]O)[C[]\T1/pcr /b/n/9 @H[]\T1/pcr/m/n/9 ](C)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ]([C []\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)O)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T 1/pcr/m/n/9 ][]2[]CSSC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](NC1[]=[]O)C([]=[]O) N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1cnc[nH][]1[])C([]=[]O)N[C[]\T1/p cr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1 /pcr/m/n/9 ](CCCNC([]=[]N)N)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1c[nH]c3ccccc13)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCNC( []=[]N)N)C([]=[]O)N2| Overfull \hbox (167.44426pt too wide) in paragraph at lines 7758--7758 []\T1/pcr/m/n/9 CN1C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCNC([]=[]N) N)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2ccc(O)cc2)NC([]=[]O)[ C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O)[C[]\T1/pcr/b/n/9 @ H[]\T1/pcr/m/n/9 ](Cc2ccc3ccccc3c2)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr /m/n/9 ][]1[]CC([]=[]O)O| Overfull \hbox (113.44432pt too wide) in paragraph at lines 7759--7759 []\T1/pcr/m/n/9 NCCCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](NC([]=[]O)[C[]\T1/pc r/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccc(OP([]=[]O)(O)O)cc1)NC([]=[]O)Cc1ccccc1)C([]= []O)N1CCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]C([]=[]O)N[C[]@[][]\T1/pcr/b /n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C(N)[]=[]O| Overfull \hbox (675.04369pt too wide) in paragraph at lines 7760--7760 []\T1/pcr/m/n/9 CCCCCCCCCCCCCCCCNC([]=[]O)CN(CC([]=[]O)NC(C)(C)C([]=[]O)N[C[]@[ ][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCNC([]=[]N)N )C([]=[]O)N1CCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]C([]=[]O)N[C[]@[][]\T1 /pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCNC([]=[]N)N)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(N)[]=[]O)C(N)[]=[]O)C([]=[]O)c1cccnc1| Overfull \hbox (491.4439pt too wide) in paragraph at lines 7761--7761 []\T1/pcr/m/n/9 CCCCCCCCCCCCCCCCN(CCCCCCCCCCCCCCCC)CCCCCC([]=[]O)NC(C)(C)C([]=[ ]O)NC(Cc1ccccc1)C([]=[]O)NC(CC(C)C)C([]=[]O)NC(Cc1ccccc1)C([]=[]O)NC(CCCNC([]=[ ]N)N)C([]=[]O)N1CCCC1C([]=[]O)NC(CCCNC([]=[]N)N)C([]=[]O)NC(CC(N)[]=[]O)C(N)[]= []O| Overfull \hbox (383.44402pt too wide) in paragraph at lines 7762--7762 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2cc ccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]@[][] \T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/p cr/m/n/9 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C(C)C)NC([ ]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCSC)NC1[]=[]O| Overfull \hbox (394.244pt too wide) in paragraph at lines 7763--7763 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2cc ccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]@[][] \T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/p cr/m/n/9 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C(C)C)NC([ ]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 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@H[]\T1/pcr/m/n/9 ][]2[]CCC N2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC[S[]+[]](C)[O[]- [119] Overfull \hbox (1096.24321pt too wide) in paragraph at lines 7778--7778 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][ ]2[]CCCN2C([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O) [C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ]([C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)CC)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CO)NC([]=[]O)[C[]\T1/pcr /b/n/9 @H[]\T1/pcr/m/n/9 ](C)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ]([C []\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)O)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T 1/pcr/m/n/9 ][]2[]CSSC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](NC1[]=[]O)C([]=[]O) N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1cnc[nH][]1[])C([]=[]O)N[C[]\T1/p cr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1 /pcr/m/n/9 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lines 7782--7782 []\T1/pcr/m/n/9 CCCCCCCCCCCCCCCCNC([]=[]O)CN(CC([]=[]O)NC(C)(C)C([]=[]O)N[C[]@[ ][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCNC([]=[]N)N )C([]=[]O)N1CCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]C([]=[]O)N[C[]@[][]\T1 /pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCNC([]=[]N)N)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(N)[]=[]O)C(N)[]=[]O)C([]=[]O)c1cccnc1| Overfull \hbox (383.44402pt too wide) in paragraph at lines 7783--7783 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2cc ccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]@[][] \T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/p cr/m/n/9 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C(C)C)NC([ ]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCSC)NC1[]=[]O| Overfull \hbox (394.244pt too wide) in paragraph at lines 7784--7784 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2cc ccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]@[][] \T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/p cr/m/n/9 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C(C)C)NC([ ]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC[S[]+[]](C)[O[]- Overfull \hbox (448.24394pt too wide) in paragraph at lines 7785--7785 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2c[ nH]c3ccccc23)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2ccccc2)NC([]=[] O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2ccccc2)NC([]=[]O)[C[]@[][]\T1/pcr/b/ n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ] (CCSC)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]\T1/ pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC[S[]+[]](C)[O[]- Overfull \hbox (270.04414pt too wide) in paragraph at lines 7786--7786 [][]\T1/pcr/m/n/9 ])NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C(C)C)NC([] =[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2c[nH]c3ccccc23)NC([]=[]O)[C[]\T1/ pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr /m/n/9 ](Cc2ccccc2)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCC N2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC[S[]+[]](C)[O[]- Overfull \hbox (550.84383pt too wide) in paragraph at lines 7787--7787 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]\T1/pcr/b/n/9 @H[ ]\T1/pcr/m/n/9 ](N)C([]=[]O)N[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C([]=[]O)N[C []@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)C([]=[]O)N[C[]\T1/pcr/b/n/9 @H[ ]\T1/pcr/m/n/9 ](C([]=[]O)N1CCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]C([]=[ ]O)N1CCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]C([]=[]O)N[C[]\T1/pcr/b/n/9 @ H[]\T1/pcr/m/n/9 ](CCC([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCC([ ]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)C([]=[]O)O)Cc1ccccc1)C c1ccccc1)C(C)C)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)CC| [120] [121] [122] Overfull \vbox (1.18257pt too high) detected at line 7995 [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] Chapter 6. [133] Underfull \hbox (badness 10000) in paragraph at lines 8641--8644 \T1/ptm/m/n/10 Uncharger::uncharge() will now neu-tral-ize \T1/pcr/m/n/10 [Cl,B r,I][O-], [Cl,Br,I](=O)[O-], [Cl,Br, Underfull \hbox (badness 10000) in paragraph at lines 8641--8644 \T1/pcr/m/n/10 I](=O)(=O)[O-], [Cl,Br,I](=O)(=O)(=O)[O-], [O-]N=N[O-], [N,P](=O )[O-], Underfull \hbox (badness 10000) in paragraph at lines 8641--8644 \T1/pcr/m/n/10 [N+](=O)([O-])[O-], P(=O)([O-])[O-], P(=O)([O-])([O-])[O-], S([O -])[O-], [134] [135] [136] Chapter 7. [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] Chapter 8. [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 10677. Underfull \hbox (badness 10000) in paragraph at lines 10677--10678 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 auto\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 keywor d here is hiding the fact that \T1/ptm/m/n/10 get-Bond-Be-tweenAtoms\T1/pcr/m/n /10 returns the [165] LaTeX Warning: Hyper reference `GettingStartedInC++:TheSSSRProblem' on page 166 undefined on input line 10793. [166] LaTeX Warning: Hyper reference `GettingStartedInC++:twoAddHs' on page 167 undef ined on input line 10820. [167] [168] LaTeX Warning: Hyper reference `GettingStartedInC++:blaney' on page 169 undefin ed on input line 10993. LaTeX Warning: Hyper reference `GettingStartedInC++:rappe' on page 169 undefine d on input line 11022. LaTeX Warning: Hyper reference `GettingStartedInC++:riniker2' on page 169 undef ined on input line 11025. [169] LaTeX Warning: Hyper reference `GettingStartedInC++:mmff1' on page 170 undefine d on input line 11066. LaTeX Warning: Hyper reference `GettingStartedInC++:mmff2' on page 170 undefine d on input line 11066. LaTeX Warning: Hyper reference `GettingStartedInC++:mmff3' on page 170 undefine d on input line 11066. LaTeX Warning: Hyper reference `GettingStartedInC++:mmff4' on page 170 undefine d on input line 11067. LaTeX Warning: Hyper reference `GettingStartedInC++:mmffs' on page 170 undefine d on input line 11067. [170] Overfull \vbox (2.2835pt too high) detected at line 11220 [171] [172] [173] [174] [175] [176] LaTeX Warning: Hyper reference `GettingStartedInC++:guba' on page 177 undefined on input line 11588. [177] [178] [179] [180] Chapter 9. [181] [182] Chapter 10. (./RDKit.ind) [183] (./RDKit.aux) LaTeX Warning: There were undefined references. ) (see the transcript file for additional information) {/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8 r.enc} Output written on RDKit.pdf (191 pages, 1671545 bytes). Transcript written on RDKit.log. Latexmk: Index file 'RDKit.idx' was written Latexmk: Log file says output to 'RDKit.pdf' Latexmk: Examining 'RDKit.log' === TeX engine is 'pdfTeX' Latexmk: All targets (RDKit.pdf) are up-to-date make[3]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/_build/latex' pdflatex finished; the PDF files are in _build/latex. make[2]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book' make[1]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4' debian/rules override_dh_auto_test make[1]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4' cp -r rdkit obj-*/ find /build/rdkit-TKP8Bz/rdkit-202009.4 -name rdchem.so /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so #export RDBASE=/build/rdkit-TKP8Bz/rdkit-202009.4 PYTHONPATH=/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/ LD_LIBRARY_PATH="/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu//lib:" PYTHONPATH=/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/:/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu//lib:" dh_auto_test dh_auto_test: warning: Compatibility levels before 10 are deprecated (level 9 in use) cd obj-x86_64-linux-gnu && make -j4 test ARGS\+=-j4 make[2]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process -j4 Test project /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu Start 1: testCoordGen Start 2: pyCoordGen Start 3: testDict Start 4: testRDValue 1/190 Test #4: testRDValue ............................ Passed 0.00 sec Start 5: testConcurrentQueue 2/190 Test #1: testCoordGen ........................... Passed 1.35 sec Start 6: testDataStructs 3/190 Test #6: testDataStructs ........................ Passed 0.08 sec Start 7: testFPB 4/190 Test #7: testFPB ................................ Passed 0.03 sec Start 8: testMultiFPB 5/190 Test #8: testMultiFPB ........................... Passed 0.10 sec Start 9: pyBV 6/190 Test #2: pyCoordGen ............................. Passed 4.74 sec Start 10: pyDiscreteValueVect 7/190 Test #3: testDict ............................... Passed 5.25 sec Start 11: pySparseIntVect 8/190 Test #10: pyDiscreteValueVect .................... Passed 1.41 sec Start 12: pyFPB 9/190 Test #11: pySparseIntVect ........................ Passed 1.69 sec Start 13: testTransforms 10/190 Test #13: testTransforms ......................... Passed 0.09 sec Start 14: testGrid 11/190 Test #14: testGrid ............................... Passed 0.21 sec Start 15: geometryTestsCatch 12/190 Test #15: geometryTestsCatch ..................... Passed 0.07 sec Start 16: testPyGeometry 13/190 Test #9: pyBV ................................... Passed 6.19 sec Start 17: testMatrices 14/190 Test #17: testMatrices ........................... Passed 0.01 sec Start 18: testConrec 15/190 Test #12: pyFPB .................................. Passed 1.72 sec Start 19: testAlignment 16/190 Test #19: testAlignment .......................... Passed 0.01 sec Start 20: pyAlignment 17/190 Test #18: testConrec ............................. Passed 0.28 sec Start 21: testOptimizer 18/190 Test #21: testOptimizer .......................... Passed 0.02 sec Start 22: testUFFForceField 19/190 Test #22: testUFFForceField ...................... Passed 0.58 sec Start 23: testMMFFForceField 20/190 Test #16: testPyGeometry ......................... Passed 1.81 sec Start 24: pyForceFieldConstraints 21/190 Test #20: pyAlignment ............................ Passed 1.56 sec Start 25: testDistGeom 22/190 Test #25: testDistGeom ........................... Passed 0.02 sec Start 26: pyDistGeom 23/190 Test #26: pyDistGeom ............................. Passed 1.79 sec Start 27: graphmolTest1 24/190 Test #24: pyForceFieldConstraints ................ Passed 3.30 sec Start 28: graphmolcpTest 25/190 Test #28: graphmolcpTest ......................... Passed 0.10 sec Start 29: graphmolqueryTest 26/190 Test #29: graphmolqueryTest ...................... Passed 0.11 sec Start 30: graphmolMolOpsTest 27/190 Test #30: graphmolMolOpsTest ..................... Passed 5.60 sec Start 31: graphmoltestChirality 28/190 Test #31: graphmoltestChirality .................. Passed 0.79 sec Start 32: graphmoltestPickler 29/190 Test #32: graphmoltestPickler .................... Passed 1.60 sec Start 33: graphmoltestPicklerGlobalSetting 30/190 Test #33: graphmoltestPicklerGlobalSetting ....... Passed 0.10 sec Start 34: graphmolIterTest 31/190 Test #34: graphmolIterTest ....................... Passed 0.10 sec Start 35: hanoiTest 32/190 Test #35: hanoiTest .............................. Passed 15.38 sec Start 36: graphmolMemTest1 33/190 Test #36: graphmolMemTest1 ....................... Passed 0.02 sec Start 37: resMolSupplierTest 34/190 Test #37: resMolSupplierTest ..................... Passed 15.10 sec Start 38: molBundleTest 35/190 Test #38: molBundleTest .......................... Passed 0.11 sec Start 39: testSGroup 36/190 Test #39: testSGroup ............................. Passed 0.52 sec Start 40: test-valgrind 37/190 Test #40: test-valgrind .......................... Passed 0.17 sec Start 41: graphmolTestsCatch 38/190 Test #41: graphmolTestsCatch ..................... Passed 0.21 sec Start 42: graphmolSGroupCatch 39/190 Test #42: graphmolSGroupCatch .................... Passed 0.11 sec Start 43: graphmolAdjustQueryCatch 40/190 Test #43: graphmolAdjustQueryCatch ............... Passed 0.40 sec Start 44: chiralityTestsCatch 41/190 Test #44: chiralityTestsCatch .................... Passed 0.12 sec Start 45: testDepictor 42/190 Test #45: testDepictor ........................... Passed 1.88 sec Start 46: pyDepictor 43/190 Test #46: pyDepictor ............................. Passed 2.70 sec Start 47: smiTest1 44/190 Test #47: smiTest1 ............................... Passed 1.29 sec Start 48: smiTest2 45/190 Test #48: smiTest2 ............................... Passed 0.10 sec Start 49: cxsmilesTest 46/190 Test #49: cxsmilesTest ........................... Passed 0.09 sec Start 50: smaTest1 47/190 Test #50: smaTest1 ............................... Passed 0.90 sec Start 51: smiTestCatch 48/190 Test #51: smiTestCatch ........................... Passed 0.29 sec Start 52: fileParsersTest1 49/190 Test #52: fileParsersTest1 ....................... Passed 38.73 sec Start 53: testMolSupplier 50/190 Test #53: testMolSupplier ........................ Passed 1.71 sec Start 54: testGeneralFileReader 51/190 Test #54: testGeneralFileReader .................. Passed 0.69 sec Start 55: testMultithreadedMolSupplier 52/190 Test #23: testMMFFForceField ..................... Passed 116.21 sec Start 56: testMolWriter 53/190 Test #56: testMolWriter .......................... Passed 3.20 sec Start 57: testTplParser 54/190 Test #57: testTplParser .......................... Passed 0.39 sec Start 58: testMol2ToMol 55/190 Test #58: testMol2ToMol .......................... Passed 0.79 sec Start 59: testSequence 56/190 Test #59: testSequence ........................... Passed 0.49 sec Start 60: testExtendedStereoParsing 57/190 Test #60: testExtendedStereoParsing .............. Passed 0.21 sec Start 61: fileParsersCatchTest 58/190 Test #61: fileParsersCatchTest ................... Passed 0.69 sec Start 62: testPropertyLists 59/190 Test #62: testPropertyLists ...................... Passed 0.21 sec Start 63: testSubstructMatch 60/190 Test #63: testSubstructMatch ..................... Passed 2.69 sec Start 64: substructTestCatch 61/190 Test #64: substructTestCatch ..................... Passed 0.22 sec Start 65: testReaction 62/190 Test #65: testReaction ........................... Passed 4.37 sec Start 66: testReactionFingerprints 63/190 Test #66: testReactionFingerprints ............... Passed 0.21 sec Start 67: testEnumeration 64/190 Test #55: testMultithreadedMolSupplier ........... Passed 43.80 sec Start 68: rxnTestCatch 65/190 Test #68: rxnTestCatch ........................... Passed 0.40 sec Start 69: pyChemReactions 66/190 Test #69: pyChemReactions ........................ Passed 3.59 sec Start 70: pyChemReactionEnumerations 67/190 Test #70: pyChemReactionEnumerations ............. Passed 9.80 sec Start 71: pyChemReactionSanitize 68/190 Test #71: pyChemReactionSanitize ................. Passed 2.00 sec Start 72: testChemTransforms 69/190 Test #72: testChemTransforms ..................... Passed 0.52 sec Start 73: chemTransformsTestCatch 70/190 Test #73: chemTransformsTestCatch ................ Passed 0.10 sec Start 74: tautomerQueryTestCatch 71/190 Test #74: tautomerQueryTestCatch ................. Passed 0.82 sec Start 75: pyTautomerQuery 72/190 Test #75: pyTautomerQuery ........................ Passed 1.79 sec Start 76: testSubgraphs1 73/190 Test #76: testSubgraphs1 ......................... Passed 1.50 sec Start 77: testSubgraphs2 74/190 Test #77: testSubgraphs2 ......................... Passed 0.11 sec Start 78: filterCatalogTest 75/190 Test #78: filterCatalogTest ...................... Passed 1.11 sec Start 79: pyFilterCatalog 76/190 Test #27: graphmolTest1 .......................... Passed 158.79 sec Start 80: testFragCatalog 77/190 Test #79: pyFilterCatalog ........................ Passed 5.89 sec Start 81: pyFragCatalog 78/190 Test #80: testFragCatalog ........................ Passed 4.71 sec Start 82: testDescriptors 79/190 Test #81: pyFragCatalog .......................... Passed 2.10 sec Start 83: testAUTOCORR2D 80/190 Test #83: testAUTOCORR2D ......................... Passed 3.00 sec Start 84: testATF 81/190 Test #84: testATF ................................ Passed 0.22 sec Start 85: testBCUT 82/190 Test #85: testBCUT ............................... Passed 8.29 sec Start 86: testEEM 83/190 Test #86: testEEM ................................ Passed 6.81 sec Start 87: testPBF 84/190 Test #87: testPBF ................................ Passed 2.38 sec Start 88: testRDFcustom 85/190 Test #82: testDescriptors ........................ Passed 25.99 sec Start 89: testRDF 86/190 Test #67: testEnumeration ........................ Passed 62.60 sec Start 90: testMORSE 87/190 Test #89: testRDF ................................ Passed 4.08 sec Start 91: test3D 88/190 Test #90: testMORSE .............................. Passed 5.08 sec Start 92: testWHIM 89/190 Test #91: test3D ................................. Passed 2.92 sec Start 93: testGETAWAY 90/190 Test #92: testWHIM ............................... Passed 2.10 sec Start 94: testAUTOCORR3D 91/190 Test #94: testAUTOCORR3D ......................... Passed 3.19 sec Start 95: testCoulombMat 92/190 Test #95: testCoulombMat ......................... Passed 0.12 sec Start 96: pyMolDescriptors 93/190 Test #96: pyMolDescriptors ....................... Passed 3.40 sec Start 97: pyMolDescriptors3D 94/190 Test #97: pyMolDescriptors3D ..................... Passed 2.58 sec Start 98: testFingerprints 95/190 Test #93: testGETAWAY ............................ Passed 17.67 sec Start 99: testMHFPFingerprint 96/190 Test #99: testMHFPFingerprint .................... Passed 0.90 sec Start 100: testFingerprintGenerators 97/190 Test #88: testRDFcustom .......................... Passed 37.41 sec Start 101: fpTestCatch 98/190 Test #101: fpTestCatch ............................ Passed 0.39 sec Start 102: pyTestGenerator 99/190 Test #100: testFingerprintGenerators .............. Passed 10.00 sec Start 103: pyTestMHFP 100/190 Test #102: pyTestGenerator ........................ Passed 3.80 sec Start 104: testPartialCharges 101/190 Test #104: testPartialCharges ..................... Passed 0.30 sec Start 105: pyPartialCharges 102/190 Test #103: pyTestMHFP ............................. Passed 5.11 sec Start 106: testMolTransforms 103/190 Test #106: testMolTransforms ...................... Passed 0.31 sec Start 107: pyMolTransforms 104/190 Test #105: pyPartialCharges ....................... Passed 5.89 sec Start 108: testMMFFForceFieldHelpers 105/190 Test #107: pyMolTransforms ........................ Passed 4.19 sec Start 109: testMMFFForceFieldHelpersMultiThread 106/190 Test #109: testMMFFForceFieldHelpersMultiThread ... Passed 4.90 sec Start 110: testUFFForceFieldHelpers 107/190 Test #98: testFingerprints ....................... Passed 46.69 sec Start 111: testCrystalForceField 108/190 Test #111: testCrystalForceField .................. Passed 1.31 sec Start 112: pyForceFieldHelpers 109/190 Test #112: pyForceFieldHelpers .................... Passed 5.39 sec Start 113: testDistGeomHelpers 110/190 Test #108: testMMFFForceFieldHelpers .............. Passed 43.70 sec Start 114: pyDistGeomHelpers 111/190 Test #110: testUFFForceFieldHelpers ............... Passed 56.89 sec Start 115: testMolAlign 112/190 Test #115: testMolAlign ........................... Passed 0.62 sec Start 116: testO3AAlign 113/190 Test #114: pyDistGeomHelpers ...................... Passed 192.60 sec Start 117: pyMolAlign 114/190 Test #116: testO3AAlign ........................... Passed 243.87 sec Start 118: testFeatures 115/190 Test #118: testFeatures ........................... Passed 0.40 sec Start 119: pyChemicalFeatures 116/190 Test #119: pyChemicalFeatures ..................... Passed 2.32 sec Start 120: testShapeHelpers 117/190 Test #120: testShapeHelpers ....................... Passed 0.21 sec Start 121: pyShapeHelpers 118/190 Test #121: pyShapeHelpers ......................... Passed 2.47 sec Start 122: testMolCatalog 119/190 Test #122: testMolCatalog ......................... Passed 0.30 sec Start 123: pyMolCatalog 120/190 Test #123: pyMolCatalog ........................... Passed 1.51 sec Start 124: moldraw2DTest1 121/190 Test #117: pyMolAlign ............................. Passed 92.50 sec Start 125: moldraw2DTestCatch 122/190 Test #125: moldraw2DTestCatch ..................... Passed 1.69 sec Start 126: moldraw2DRxnTest1 123/190 Test #126: moldraw2DRxnTest1 ...................... Passed 1.91 sec Start 127: pyMolDraw2D 124/190 Test #127: pyMolDraw2D ............................ Passed 6.80 sec Start 128: testFMCS 125/190 Test #124: moldraw2DTest1 ......................... Passed 43.79 sec Start 129: pyFMCS 126/190 Test #128: testFMCS ............................... Passed 21.91 sec Start 130: FMCStest 127/190 Test #130: FMCStest ............................... Passed 0.19 sec Start 131: molHashCatchTest 128/190 Test #131: molHashCatchTest ....................... Passed 0.11 sec Start 132: pyMolHash 129/190 Test #132: pyMolHash .............................. Passed 1.40 sec Start 133: testMMPA 130/190 Test #133: testMMPA ............................... Passed 0.49 sec Start 134: pyMMPA 131/190 Test #134: pyMMPA ................................. Passed 8.20 sec Start 135: testCIPLabeler 132/190 Test #135: testCIPLabeler ......................... Passed 0.20 sec Start 136: pyCIPLabelsWrapTest 133/190 Test #136: pyCIPLabelsWrapTest .................... Passed 1.30 sec Start 137: pyCIPLabelsValidation 134/190 Test #129: pyFMCS ................................. Passed 20.81 sec Start 138: deprotectTest 135/190 Test #138: deprotectTest .......................... Passed 0.20 sec Start 139: pyDeprotect 136/190 Test #139: pyDeprotect ............................ Passed 1.90 sec Start 140: testReducedGraphs 137/190 Test #140: testReducedGraphs ...................... Passed 0.29 sec Start 141: pyReducedGraphs 138/190 Test #141: pyReducedGraphs ........................ Passed 1.40 sec Start 142: trajectoryTest 139/190 Test #142: trajectoryTest ......................... Passed 1.91 sec Start 143: substructLibraryTest 140/190 Test #143: substructLibraryTest ................... Passed 11.57 sec Start 144: pySubstructLibrary 141/190 Test #137: pyCIPLabelsValidation .................. Passed 35.19 sec Start 145: testRGroupDecomp 142/190 Test #113: testDistGeomHelpers .................... Passed 384.41 sec Start 146: pyRGroupDecomposition 143/190 Test #145: testRGroupDecomp .......................Child aborted***Exception: 10.30 sec [17:26:08] ******************************************************** [17:26:08] Testing R-Group Decomposition [17:26:08] ******************************************************** [17:26:08] test rgroup decomp symmetry matching [17:26:08] ******************************************************** [17:26:08] test rgroup decomp rgroup only matching [17:26:08] ******************************************************** [17:26:08] test rgroup decomp ring matching [17:26:08] ******************************************************** [17:26:08] test rgroup decomp full ring dummy core [17:26:08] ******************************************************** [17:26:08] test multi core [17:26:09] ******************************************************** [17:26:09] test Github #1550: Kekulization error from R-group decomposition [17:26:09] ******************************************************** [17:26:09] test remove sidechain Hs [17:26:09] ******************************************************** [17:26:09] test matching only rgroups but allows Hs [17:26:09] ******************************************************** [17:26:09] test rgroup decomp full ring dummy core [17:26:09] ******************************************************** [17:26:09] test grouping substituents in chunks as large as possible [17:26:09] ******************************************************** [17:26:09] test github #2332: RGroupDecomposition: addHs() call should set coords [17:26:09] ******************************************************** [17:26:09] test a problem with row-column alignment [17:26:09] ******************************************************** [17:26:09] Testing R-Group symmetry issues [17:26:09] ******************************************************** [17:26:09] Testing R-Group symmetry issues iterative bulk bulk, no symmetry [17:26:18] **** Test Assert Expression Failed: Violation occurred on line 1190 in file ./Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp Failed Expression: ok **** terminate called after throwing an instance of 'Invar::Invariant' what(): Expression Failed: Start 147: molInterchangeTest1 144/190 Test #147: molInterchangeTest1 .................... Passed 0.12 sec Start 148: pyMolInterchange 145/190 Test #148: pyMolInterchange ....................... Passed 1.79 sec Start 149: testSLNParse 146/190 Test #149: testSLNParse ........................... Passed 0.29 sec Start 150: pySLNParse 147/190 Test #146: pyRGroupDecomposition .................. Passed 10.22 sec Start 151: pyGraphMolWrap 148/190 Test #150: pySLNParse ............................. Passed 1.70 sec Start 152: pyTestConformerWrap 149/190 Test #152: pyTestConformerWrap .................... Passed 1.80 sec Start 153: pyTestTrajectory 150/190 Test #153: pyTestTrajectory ....................... Passed 3.71 sec Start 154: pyTestSGroups 151/190 Test #154: pyTestSGroups .......................... Passed 1.71 sec Start 155: pyTestThreads 152/190 Test #155: pyTestThreads .......................... Passed 11.19 sec Start 156: pyTestMultithreadedMolSupplier 153/190 Test #144: pySubstructLibrary ..................... Passed 43.42 sec Start 157: pyTestPropertyLists 154/190 Test #157: pyTestPropertyLists .................... Passed 1.79 sec Start 158: molStandardizeTest 155/190 Test #156: pyTestMultithreadedMolSupplier ......... Passed 1.90 sec Start 159: molNormalizeTest 156/190 Test #159: molNormalizeTest ....................... Passed 0.60 sec Start 160: molValidateTest 157/190 Test #160: molValidateTest ........................ Passed 0.41 sec Start 161: molChargeTest 158/190 Test #161: molChargeTest .......................... Passed 0.59 sec Start 162: molTautomerTest 159/190 Test #158: molStandardizeTest ..................... Passed 4.90 sec Start 163: molStandardizeSmallTest 160/190 Test #163: molStandardizeSmallTest ................ Passed 0.31 sec Start 164: molFragmentTest 161/190 Test #164: molFragmentTest ........................ Passed 0.39 sec Start 165: molStandardizeCatchTest 162/190 Test #165: molStandardizeCatchTest ................ Passed 0.48 sec Start 166: pyMolStandardize 163/190 Test #5: testConcurrentQueue .................... Passed 699.95 sec Start 167: testScaffoldNetwork 164/190 Test #162: molTautomerTest ........................ Passed 14.80 sec Start 168: pyScaffoldNetwork 165/190 Test #168: pyScaffoldNetwork ...................... Passed 2.50 sec Start 169: pyScaffoldNetworkPickling 166/190 Test #167: testScaffoldNetwork .................... Passed 6.70 sec Start 170: testMolEnumerator 167/190 Test #166: pyMolStandardize ....................... Passed 14.01 sec Start 171: pyMolEnumerator 168/190 Test #170: testMolEnumerator ...................... Passed 0.29 sec Start 172: testAbbreviations 169/190 Test #172: testAbbreviations ...................... Passed 0.20 sec Start 173: pyAbbreviations 170/190 Test #169: pyScaffoldNetworkPickling .............. Passed 2.00 sec Start 174: testQuery 171/190 Test #174: testQuery .............................. Passed 0.09 sec Start 175: testMatCalc 172/190 Test #175: testMatCalc ............................ Passed 0.01 sec Start 176: pyMatCalc 173/190 Test #171: pyMolEnumerator ........................ Passed 2.00 sec Start 177: testSimDivPickers 174/190 Test #177: testSimDivPickers ...................... Passed 0.09 sec Start 178: pickersTestsCatch 175/190 Test #173: pyAbbreviations ........................ Passed 2.19 sec Start 179: pySimDivPickers 176/190 Test #178: pickersTestsCatch ...................... Passed 0.79 sec Start 180: pyRanker 177/190 Test #180: pyRanker ............................... Passed 2.11 sec Start 181: testChemicalFeatures 178/190 Test #181: testChemicalFeatures ................... Passed 0.00 sec Start 182: pyFeatures 179/190 Test #176: pyMatCalc .............................. Passed 4.49 sec Start 183: pythonTestDbCLI 180/190 Test #182: pyFeatures ............................. Passed 2.59 sec Start 184: pythonTestDirML 181/190 Test #151: pyGraphMolWrap ......................... Passed 49.28 sec Start 185: pythonTestDirDataStructs 182/190 Test #179: pySimDivPickers ........................ Passed 9.71 sec Start 186: pythonTestDirDbase 183/190 Test #185: pythonTestDirDataStructs ............... Passed 7.81 sec Start 187: pythonTestDirSimDivFilters 184/190 Test #186: pythonTestDirDbase ..................... Passed 4.71 sec Start 188: pythonTestDirVLib 185/190 Test #187: pythonTestDirSimDivFilters ............. Passed 2.59 sec Start 189: pythonTestDirChem 186/190 Test #188: pythonTestDirVLib ...................... Passed 4.10 sec Start 190: pythonTestSping 187/190 Test #190: pythonTestSping ........................ Passed 4.90 sec 188/190 Test #184: pythonTestDirML ........................ Passed 98.70 sec 189/190 Test #183: pythonTestDbCLI ........................ Passed 110.30 sec 190/190 Test #189: pythonTestDirChem ...................... Passed 237.95 sec 99% tests passed, 1 tests failed out of 190 Total Test time (real) = 963.63 sec The following tests FAILED: 145 - testRGroupDecomp (Child aborted) Errors while running CTest make[2]: *** [Makefile:129: test] Error 8 make[2]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j4 test ARGS\+=-j4 returned exit code 2 make[1]: [debian/rules:126: override_dh_auto_test] Error 25 (ignored) make[1]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4' fakeroot debian/rules binary-arch dh binary-arch --with python3 --buildsystem=cmake --parallel dh: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_testroot -a -O--buildsystem=cmake -O--parallel dh_prep -a -O--buildsystem=cmake -O--parallel debian/rules override_dh_auto_install make[1]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4' dh_auto_install dh_auto_install: warning: Compatibility levels before 10 are deprecated (level 9 in use) cd obj-x86_64-linux-gnu && make -j4 install DESTDIR=/build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/rdkit-TKP8Bz/rdkit-202009.4 -B/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/CMakeFiles /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/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 -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/depend make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/External/catch /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/catch /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/catch/CMakeFiles/catch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/External/INCHI-API /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/INCHI-API /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/External/CoordGen /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/External/RingFamilies /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/RingFamilies /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.dir/build make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'External/catch/CMakeFiles/catch.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'External/CoordGen/CMakeFiles/coordgen_support.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E copy /build/rdkit-TKP8Bz/rdkit-202009.4/External/INCHI-API/python/noinchi.py /build/rdkit-TKP8Bz/rdkit-202009.4/rdkit/Chem/inchi.py [ 0%] Built target catch [ 0%] Built target coordgen_support [ 0%] Built target ringdecomposerlib_support make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/depend make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDStreams /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDStreams /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDStreams/CMakeFiles/RDStreams.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/Cluster/Murtagh /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake --color= [ 0%] Built target inchi_support make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/RDStreams/CMakeFiles/RDStreams.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/RDGeneral/CMakeFiles/RDGeneral.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 0%] Built target hc [ 0%] Built target RDStreams [ 1%] Built target RDGeneral make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDBoost /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/EigenSolvers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/RDBoost/CMakeFiles/RDBoost.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/DataStructs/CMakeFiles/DataStructs.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 1%] Built target testConcurrentQueue make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake --color= [ 1%] Built target RDBoost make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend [ 2%] Built target EigenSolvers [ 3%] Built target DataStructs make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/RDGeneral /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu 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'/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/RDGeneral/CMakeFiles/testRDValue.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/RDGeneral/CMakeFiles/testDict.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/DataStructs/CMakeFiles/testMultiFPB.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 3%] Built target testDict [ 3%] Built target testMultiFPB make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend [ 4%] Built target rdBase [ 4%] Built target testRDValue make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake --color= make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataStructs/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/DataStructs/CMakeFiles/testDataStructs.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/DataStructs/CMakeFiles/testFPB.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Numerics/CMakeFiles/testMatrices.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build [ 4%] Built target testMatrices [ 4%] Built target testFPB [ 5%] Built target testDataStructs make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Catalogs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Catalogs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Query /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Query /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataManip/MetricMatrixCalc /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake --color= [ 7%] Built target cDataStructs make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Query/CMakeFiles/testQuery.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build [ 7%] Built target testQuery [ 8%] Built target testMatCalc make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Catalogs/CMakeFiles/Catalogs.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' 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-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/Cluster/Murtagh /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake --color= [ 8%] Built target Catalogs make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ML/InfoTheory /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build 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-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 9%] Built target SimDivPickers make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= [ 9%] Built target rdMetricMatrixCalc [ 9%] Built target Clustering make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Geometry/CMakeFiles/RDGeometryLib.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 10%] Built target RDGeometryLib make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/SimDivPickers/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake --color= [ 10%] Built target InfoTheory make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/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-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ChemicalFeatures /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 10%] Built target pickersTestsCatch make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend [ 10%] Built target testSimDivPickers make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Alignment /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 10%] Built target ChemicalFeatures make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build [ 11%] Built target Alignment [ 11%] Built target rdSimDivPickers make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/GraphMol.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 15%] Built target GraphMol [ 15%] Built target geometryTestsCatch make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Geometry/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Geometry/CMakeFiles/testGrid.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Geometry/CMakeFiles/testTransforms.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 15%] Built target testGrid make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Alignment /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake --color= [ 15%] Built target testTransforms make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Alignment/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Numerics/CMakeFiles/testConrec.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 16%] Built target testConrec make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 17%] Built target rdGeometry make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Trajectory /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Subgraphs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build [ 17%] Built target testAlignment make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build'. make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/PartialCharges /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 17%] Built target Trajectory [ 17%] Built target rdAlignment [ 17%] Built target Subgraphs make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolCatalog /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolInterchange /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 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'/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 18%] Built target PartialCharges make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SLNParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse 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'/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 18%] Built target MolInterchange make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend [ 19%] Built target MolCatalog make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake --color= make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 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/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Data /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 23%] Built target rdtrajectory [ 23%] Built target rdqueries make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ChemicalFeatures /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ChemicalFeatures/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/build [ 23%] Built target rdInfoTheory make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/ML/Data/CMakeFiles/cQuantize.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolTransforms /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake --color= make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 23%] Built target cQuantize make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend [ 23%] Built target testChemicalFeatures make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Substruct /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= [ 23%] Built target rdChemicalFeatures make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Optimizer /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build [ 23%] Built target MolTransforms make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/PartialCharges/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build [ 23%] Built target SubstructMatch make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend [ 23%] Built target Optimizer make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolTransforms/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ShapeHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 24%] Built target rdPartialCharges [ 24%] Built target SmilesParse make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolCatalog/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 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'/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build [ 24%] Built target rdMolCatalog make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/CIPLabeler/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake --color= [ 25%] Built target ShapeHelpers [ 27%] Built target testCIPLabeler make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ReducedGraphs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolInterchange/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 28%] Built target rdMolTransforms make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SLNParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake --color= [ 28%] Built target rdCIPLabeler make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SLNParse/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 28%] Built target ReducedGraphs [ 28%] Built target testSLNParse [ 28%] Built target rdMolInterchange make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Abbreviations /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemTransforms /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake --color= make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 29%] Built target rdSLNParse make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/Numerics/Optimizer /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 29%] Built target ChemTransforms [ 29%] Built target Abbreviations make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend [ 30%] Built target testOptimizer make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake --color= [ 30%] Built target MolAlign make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/test-valgrind.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 30%] Built target test-valgrind make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build [ 30%] Built target graphmolcpTest make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend [ 30%] Built target graphmolqueryTest make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/ForceField/CMakeFiles/ForceField.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build [ 33%] Built target ForceField make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake --color= [ 33%] Built target smaTest1 make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake --color= [ 33%] Built target graphmolMemTest1 make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend [ 33%] Built target graphmolIterTest make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Subgraphs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 34%] Built target smiTest2 make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Subgraphs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 36%] Built target Fingerprints make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/DependInfo.cmake --color= [ 37%] Built target testSubgraphs2 [ 38%] Built target FilterCatalog make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake --color= [ 38%] Built target testSubgraphs1 make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/PartialCharges /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 38%] Built target rdMHFPFingerprint make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend [ 39%] Built target FragCatalog make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build [ 40%] Built target rdFingerprintGenerator make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ShapeHelpers/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ReducedGraphs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build [ 40%] Built target testPartialCharges make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ReducedGraphs/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build [ 41%] Built target MolChemicalFeatures [ 41%] Built target testReducedGraphs make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build [ 41%] Built target rdShapeHelpers make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Abbreviations/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 41%] Built target rdReducedGraphs make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend [ 42%] Built target SubstructLibrary make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/External/CoordGen/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 43%] Built target rdAbbreviations make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake --color= [ 45%] Built target rdchem make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 45%] Built target Depictor make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 46%] Built target rdfiltercatalog make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake --color= make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake --color= [ 46%] Built target rdCoordGen make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend [ 47%] Built target ForceFieldHelpers make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 48%] Built target rdMolChemicalFeatures [ 48%] Built target rdSubstructLibrary make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 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/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake --color= make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build [ 49%] Built target rdDepictor make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend [ 52%] Built target FileParsers make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 52%] Built target rdForceFieldHelpers make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build [ 52%] Built target O3AAlign make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/DistGeom/CMakeFiles/DistGeometry.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 52%] Built target rdForceField make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend [ 53%] Built target DistGeometry make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake --color= make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/depend [ 53%] Built target chiralityTestsCatch make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 53%] Built target graphmolSGroupCatch make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/testSGroup.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake --color= [ 54%] Built target graphmolTestsCatch make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake --color= [ 55%] Built target graphmolAdjustQueryCatch [ 55%] Built target testSGroup make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake --color= make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 55%] Built target graphmoltestPicklerGlobalSetting make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolTest1.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 55%] Built target graphmolTest1 [ 55%] Built target graphmoltestChirality [ 57%] Built target resMolSupplierTest [ 57%] Built target graphmoltestPickler make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Depictor /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/molBundleTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/hanoiTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 58%] Built target graphmolMolOpsTest make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake --color= [ 58%] Built target testDepictor [ 59%] Built target hanoiTest [ 59%] Built target molBundleTest make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build [ 59%] Built target smiTest1 make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 60%] Built target testMolWriter make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build [ 61%] Built target cxsmilesTest [ 61%] Built target smiTestCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 62%] Built target testSequence make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 62%] Built target testMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build [ 63%] Built target fileParsersTest1 make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 63%] Built target testMultithreadedMolSupplier make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake --color= [ 64%] Built target testExtendedStereoParsing make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 65%] Built target testGeneralFileReader make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 65%] Built target fileParsersCatchTest make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend [ 65%] Built target testTplParser [ 65%] Built target testMol2ToMol make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Substruct /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake --color= make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Substruct /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 66%] Built target testPropertyLists make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemTransforms /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build [ 66%] Built target testSubstructMatch make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend [ 66%] Built target substructTestCatch make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemTransforms /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FilterCatalog /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 66%] Built target testChemTransforms make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 66%] Built target chemTransformsTestCatch make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend [ 68%] Built target Descriptors make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake --color= [ 68%] Built target filterCatalogTest [ 68%] Built target testFragCatalog make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 68%] Built target testMHFPFingerprint make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend [ 68%] Built target rdfragcatalog [ 68%] Built target fpTestCatch make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Fingerprints /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake --color= make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake --color= cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolTransforms /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake --color= [ 69%] Built target testFingerprintGenerators make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 69%] Built target testFingerprints make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ShapeHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 69%] Built target testFeatures make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend [ 69%] Built target testMolTransforms [ 69%] Built target rdMolAlign make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolCatalog /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolHash /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 71%] Built target MolHash [ 71%] Built target testMolCatalog make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MMPA /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Trajectory /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake --color= [ 72%] Built target testShapeHelpers [ 72%] Built target FMCS make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/SubstructLibrary /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolInterchange /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build [ 73%] Built target trajectoryTest [ 73%] Built target MMPA make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Abbreviations /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake --color= [ 73%] Built target substructLibraryTest make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/External/CoordGen /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build [ 74%] Built target molInterchangeTest1 make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/UFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake --color= [ 74%] Built target testAbbreviations make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/DistGeomHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build [ 76%] Built target rdmolfiles make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'External/CoordGen/CMakeFiles/testCoordGen.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/DistGeom/CMakeFiles/testDistGeom.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 76%] Built target testCoordGen [ 77%] Built target testDistGeom make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend [ 77%] Built target DistGeomHelpers make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/DistGeom/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake --color= [ 78%] Built target testUFFForceField make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 78%] Built target testAUTOCORR3D make -f Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/depend [ 78%] Built target testMORSE [ 79%] Built target DistGeom make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/DependInfo.cmake --color= cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/DependInfo.cmake --color= [ 82%] Built target ChemReactions make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 82%] Built target testGETAWAY make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/DependInfo.cmake --color= [ 83%] Built target testAUTOCORR2D [ 83%] Built target testDescriptors make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/DependInfo.cmake --color= [ 83%] Built target testATF make -f Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 83%] Built target testEEM make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make 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'/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/DependInfo.cmake --color= make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build [ 84%] Built target testBCUT make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 84%] Built target testWHIM make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build [ 84%] Built target testRDF make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend [ 84%] Built target rdMolDescriptors make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake --color= make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build [ 84%] Built target testMMFFForceFieldHelpersMultiThread make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/DistGeomHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 85%] Built target testMMFFForceFieldHelpers make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend [ 85%] Built target testUFFForceFieldHelpers make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 85%] Built target testCrystalForceField make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolAlign /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake --color= [ 85%] Built target testDistGeomHelpers make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 85%] Built target rdDistGeom make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake --color= [ 85%] Built target testO3AAlign make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake --color= [ 85%] Built target testMolAlign make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/FMCS/Test /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 87%] Built target MolDraw2D make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend [ 87%] Built target testFMCS [ 87%] Built target rdFMCS make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolHash /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake --color= make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolHash/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MMPA /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build [ 87%] Built target FMCStest make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MMPA/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build'. make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 87%] Built target rdMolHash make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Deprotect /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake --color= [ 87%] Built target molHashCatchTest make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend [ 87%] Built target testMMPA make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 88%] Built target rdMMPA [ 89%] Built target Deprotect make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 90%] Built target RGroupDecomposition make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/ForceField/MMFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/MMFF /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake --color= [ 90%] Built target MolEnumerator make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake --color= [ 90%] Built target rdmolops make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 90%] Built target testReactionFingerprints make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend [ 90%] Built target testReaction make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake --color= [ 90%] Built target testEnumeration make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake --color= make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake --color= [ 90%] Built target testMMFFForceField make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build [ 91%] Built target rxnTestCatch [ 91%] Built target rdChemReactions make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 94%] Built target testCoulombMat [ 94%] Built target MolStandardize make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 94%] Built target moldraw2DRxnTest1 [ 94%] Built target moldraw2DTestCatch make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/depend make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Deprotect /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/Deprotect/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 95%] Built target rdMolDraw2D make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake --color= [ 95%] Built target rdDeprotect [ 95%] Built target deprotectTest make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake --color= [ 96%] Built target moldraw2DTest1 make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake --color= make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build [ 96%] Built target testRGroupDecomp make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Built target molStandardizeTest [ 97%] Built target rdRGroupDecomposition make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend [ 97%] Built target molNormalizeTest make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake --color= make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake --color= [ 97%] Built target molValidateTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 97%] Built target molChargeTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake --color= [ 97%] Built target molTautomerTest [ 97%] Built target molFragmentTest make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake --color= make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build [ 97%] Built target molStandardizeCatchTest make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build [ 97%] Built target molStandardizeSmallTest make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/MolEnumerator/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake --color= [ 99%] Built target rdMolStandardize [ 99%] Built target ScaffoldNetwork make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/TautomerQuery /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake --color= [ 99%] Built target testMolEnumerator make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 99%] Built target rdMolEnumerator [ 99%] Built target TautomerQuery make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend [ 99%] Built target testScaffoldNetwork make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/TautomerQuery/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-TKP8Bz/rdkit-202009.4 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/GraphMol/TautomerQuery /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake --color= [ 99%] Built target rdScaffoldNetwork make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build'. make[4]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' [ 99%] Built target rdTautomerQuery [100%] Built target tautomerQueryTestCatch make[3]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Numerics -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Numerics/__init__.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Avalon -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Avalon/__init__.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/DistanceGeometry -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/DistanceGeometry/__init__.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/six.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart/__init__.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart/Fontmapping.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart/pidPyart.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/__init__.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples/formatted-strings.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/pagesizes.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/__init__.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/pidPS.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/psmetrics.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/fontinfo.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/latin1MetricsCache.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/ReportLab -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/ReportLab/__init__.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/ReportLab/pidReportLab.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/patches -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/patches/Imaging-1.1.1.diff -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/stringformat.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/pid.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/TK -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/TK/__init__.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/TK/pidTK.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/__init__.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfutils.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfmetrics.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfdoc.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfgen.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfgeom.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pidPDF.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/README -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/SVG -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/SVG/__init__.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/SVG/pidSVG.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt/__init__.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt/pidQt4.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt/pidQt.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/colors.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/utils.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/WX -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/WX/__init__.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/WX/pidWxDc.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/WX/pidWX.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/util -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/util/HTMLPiddler.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/util/__init__.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/pstests.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/__init__.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/pidtest.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/testallps.ps -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/__pycache__ -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/__pycache__/pidtest.cpython-39.pyc -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/__pycache__/pstests.cpython-39.pyc -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/testallps.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/__pycache__ -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/__init__.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pidPIL.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/metrics.dat -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-12.pil -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/removemedium.py -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-10.pil -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-24.pil -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm -- Installing: 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/build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitFMCS.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FMCS/FMCS.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FMCS/Graph.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdFMCS.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolHash.so.1.2020.09.4 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolHash.so.1 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolHash.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolHash/MolHash.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolHash/nmmolhash.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMolHash.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMMPA.so.1.2020.09.4 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMMPA.so.1 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMMPA.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MMPA/MMPA.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMMPA.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1.2020.09.4 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitCIPLabeler.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/CIPLabeler/CIPLabeler.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdCIPLabeler.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitDeprotect.so.1.2020.09.4 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitDeprotect.so.1 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitDeprotect.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Deprotect/Deprotect.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdDeprotect.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1.2020.09.4 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitReducedGraphs.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ReducedGraphs/ReducedGraphs.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdReducedGraphs.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitTrajectory.so.1.2020.09.4 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitTrajectory.so.1 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitTrajectory.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Snapshot.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Trajectory.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1.2020.09.4 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSubstructLibrary.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrary.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/PatternFactory.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdSubstructLibrary.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so.1.2020.09.4 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so.1 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/RGroupDecomposition/RGroupDecomp.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdRGroupDecomposition.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolInterchange.so.1.2020.09.4 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolInterchange.so.1 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolInterchange.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolInterchange/MolInterchange.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolInterchange/details.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMolInterchange.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSLNParse.so.1.2020.09.4 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSLNParse.so.1 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSLNParse.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNAttribs.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNParse.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNParseOps.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdSLNParse.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdchem.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdmolops.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdqueries.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdmolfiles.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdtrajectory.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolStandardize.so.1.2020.09.4 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolStandardize.so.1 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolStandardize.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/MolStandardize.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Metal.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Normalize.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Validate.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Charge.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Tautomer.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Fragment.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/rdMolStandardize.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so.1.2020.09.4 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so.1 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Scaffolds/rdScaffoldNetwork.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolEnumerator.so.1.2020.09.4 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolEnumerator.so.1 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolEnumerator.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolEnumerator/MolEnumerator.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMolEnumerator.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitAbbreviations.so.1.2020.09.4 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitAbbreviations.so.1 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitAbbreviations.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Abbreviations/Abbreviations.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdAbbreviations.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/AndQuery.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/EqualityQuery.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/GreaterEqualQuery.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/GreaterQuery.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/LessEqualQuery.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/LessQuery.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/NullQueryAlgebra.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/OrQuery.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/Query.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/QueryObjects.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/RangeQuery.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/SetQuery.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/XOrQuery.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/Features/Feature.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricFuncs.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricMatrixCalc.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip/Metric/rdMetricMatrixCalc.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1.2020.09.4 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSimDivPickers.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/SimDivPickers/DistPicker.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/SimDivPickers/LeaderPicker.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/SimDivPickers/HierarchicalClusterPicker.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/SimDivPickers/MaxMinPicker.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters/rdSimDivPickers.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKithc.so.1.2020.09.4 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKithc.so.1 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKithc.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Clustering.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitInfoTheory.so.1.2020.09.4 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitInfoTheory.so.1 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitInfoTheory.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/rdInfoTheory.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/cQuantize.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1.2020.09.4 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1 -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/libRDKitChemicalFeatures.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/ChemicalFeatures/ChemicalFeature.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/include/rdkit/ChemicalFeatures/FreeChemicalFeature.h -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdChemicalFeatures.so -- Installing: /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/RDPaths.py make[2]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4' debian/rules override_dh_install make[1]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4' ln -sf /usr/share/fonts/truetype/freefont/FreeSans.ttf /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/FreeSans.ttf dh_install -ppython3-rdkit /usr/lib/python3 dh_install: warning: Compatibility levels before 10 are deprecated (level 9 in use) rm -f -rf /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/docs/ rm -f -rf /build/rdkit-TKP8Bz/rdkit-202009.4/debian/tmp/usr/share/RDKit/Projects/__pycache__ dh_numpy3 dh_install --list-missing dh_install: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_install: warning: Please use dh_missing --list-missing/--fail-missing instead dh_install: warning: This feature will be removed in compat 12. dh_missing: warning: usr/lib/cmake/rdkit/rdkit-config-version.cmake exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/cmake/rdkit/rdkit-config.cmake exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/cmake/rdkit/rdkit-targets-none.cmake exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/cmake/rdkit/rdkit-targets.cmake exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_Correlation.csv exists in debian/tmp but is not installed to anywhere 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usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_7.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_8.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_9.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/terminology_jp.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/CIPLabeling.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/Chem/FragmentCatalogs.html exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.ai exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.jpg exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.ai exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.jpg exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/CodingStandards.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/EnhancedStereo.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/SGroups.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/gsocGeneralFileReader.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_and_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_and_expand.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_or_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_expand.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_expand.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_expand.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_cis_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_or2_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_trans_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo.ai exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo.inkscape.svg exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo.lrg.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo_plain.inkscape.svg exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo_plain.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/wiki/morganfp_atomenv1.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/FingerprintGenerators.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/MolStandardize.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-DummyCores.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GenericCores.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-MutipleCores.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-RingSubstitution.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-StereoChemTest.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-example-lactam.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/compounds.txt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/RD.css exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/README exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/FeatFinderCLI.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/PythonFormat.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/README.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/create_deb_packages.sh exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/test.sh exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/license.txt exists in debian/tmp but is not installed to anywhere The following debhelper tools have reported what they installed (with files per package) * dh_install: librdkit-dev (54), librdkit1 (106), postgresql-13-rdkit (0), python3-rdkit (1), rdkit-data (3), rdkit-doc (0) If the missing files are installed by another tool, please file a bug against it. When filing the report, if the tool is not part of debhelper itself, please reference the "Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+). (in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.gz) Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built If the omission is intentional or no other helper can take care of this consider adding the paths to debian/not-installed. mkdir -p /build/rdkit-TKP8Bz/rdkit-202009.4/debian/rdkit-doc/usr/share/doc/rdkit/ cp /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/_build/latex/RDKit.pdf /build/rdkit-TKP8Bz/rdkit-202009.4/debian/rdkit-doc/usr/share/doc/rdkit/ cp -a /build/rdkit-TKP8Bz/rdkit-202009.4/Docs/Book/_build/html /build/rdkit-TKP8Bz/rdkit-202009.4/debian/rdkit-doc/usr/share/doc/rdkit/ pg_buildext install /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit build-%v postgresql-%v-rdkit ### PostgreSQL 13 install ### make[2]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4/build-13' /bin/mkdir -p '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib' /bin/mkdir -p '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/share/postgresql/13/extension' /bin/mkdir -p '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/share/postgresql/13/extension' /usr/bin/install -c -m 755 rdkit.so '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/rdkit.so' /usr/bin/install -c -m 644 /build/rdkit-TKP8Bz/rdkit-202009.4/Code/PgSQL/rdkit/rdkit.control '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/share/postgresql/13/extension/' /usr/bin/install -c -m 644 rdkit--3.8.sql '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/share/postgresql/13/extension/' /bin/mkdir -p '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode/rdkit' /bin/mkdir -p '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/ /usr/bin/install -c -m 644 rdkit_io.bc '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 mol_op.bc '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bfp_op.bc '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 sfp_op.bc '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 rxn_op.bc '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 rdkit_gist.bc '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bfp_gist.bc '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bfp_gin.bc '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 low_gist.bc '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 guc.bc '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 cache.bc '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 adapter.bc '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bitstring.bc '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ cd '/build/rdkit-TKP8Bz/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode' && /usr/lib/llvm-11/bin/llvm-lto -thinlto -thinlto-action=thinlink -o rdkit.index.bc rdkit/rdkit_io.bc rdkit/mol_op.bc rdkit/bfp_op.bc rdkit/sfp_op.bc rdkit/rxn_op.bc rdkit/rdkit_gist.bc rdkit/bfp_gist.bc rdkit/bfp_gin.bc rdkit/low_gist.bc rdkit/guc.bc rdkit/cache.bc rdkit/adapter.bc rdkit/bitstring.bc make[2]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4/build-13' ### End 13 install ### ln -sf /usr/share/javascript/jquery/jquery.js /build/rdkit-TKP8Bz/rdkit-202009.4/debian/rdkit-doc/usr/share/doc/rdkit//html/cppapi/jquery.js ln -sf /usr/share/javascript/jquery/jquery.js /build/rdkit-TKP8Bz/rdkit-202009.4/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/jquery.js ln -sf /usr/share/javascript/underscore/underscore.js /build/rdkit-TKP8Bz/rdkit-202009.4/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/underscore.js make[1]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4' dh_installdocs -a -O--buildsystem=cmake -O--parallel dh_installdocs: warning: Compatibility levels before 10 are deprecated (level 9 in use) debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4' dh_installchangelogs ReleaseNotes.md make[1]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4' debian/rules override_dh_python3 make[1]: Entering directory '/build/rdkit-TKP8Bz/rdkit-202009.4' dh_python3 -ppython3-rdkit I: dh_python3 fs:343: renaming rdBase.so to rdBase.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdAlignment.so to rdAlignment.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming DistGeom.so to DistGeom.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdAbbreviations.so to rdAbbreviations.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdCIPLabeler.so to rdCIPLabeler.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdChemReactions.so to rdChemReactions.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdChemicalFeatures.so to rdChemicalFeatures.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdCoordGen.so to rdCoordGen.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdDepictor.so to rdDepictor.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdDeprotect.so to rdDeprotect.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdDistGeom.so to rdDistGeom.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdFMCS.so to rdFMCS.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdFingerprintGenerator.so to rdFingerprintGenerator.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdForceFieldHelpers.so to rdForceFieldHelpers.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdMHFPFingerprint.so to rdMHFPFingerprint.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdMMPA.so to rdMMPA.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdMolAlign.so to rdMolAlign.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdMolCatalog.so to rdMolCatalog.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdMolChemicalFeatures.so to rdMolChemicalFeatures.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdMolDescriptors.so to rdMolDescriptors.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdMolEnumerator.so to rdMolEnumerator.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdMolHash.so to rdMolHash.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdMolInterchange.so to rdMolInterchange.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdMolTransforms.so to rdMolTransforms.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdPartialCharges.so to rdPartialCharges.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdRGroupDecomposition.so to rdRGroupDecomposition.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdReducedGraphs.so to rdReducedGraphs.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdSLNParse.so to rdSLNParse.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdShapeHelpers.so to rdShapeHelpers.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdSubstructLibrary.so to rdSubstructLibrary.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdTautomerQuery.so to rdTautomerQuery.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdchem.so to rdchem.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdfiltercatalog.so to rdfiltercatalog.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdfragcatalog.so to rdfragcatalog.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdmolfiles.so to rdmolfiles.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdmolops.so to rdmolops.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdqueries.so to rdqueries.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdtrajectory.so to rdtrajectory.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdScaffoldNetwork.so to rdScaffoldNetwork.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdMolDraw2D.so to rdMolDraw2D.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdMolStandardize.so to rdMolStandardize.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdGeometry.so to rdGeometry.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdForceField.so to rdForceField.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming Clustering.so to Clustering.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdInfoTheory.so to rdInfoTheory.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming cQuantize.so to cQuantize.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:343: renaming cDataStructs.so to cDataStructs.cpython-39-x86_64-linux-gnu.so dh_numpy3 -ppython3-rdkit make[1]: Leaving directory '/build/rdkit-TKP8Bz/rdkit-202009.4' dh_installinit -a -O--buildsystem=cmake -O--parallel dh_installinit: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_lintian -a -O--buildsystem=cmake -O--parallel dh_lintian: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_perl -a -O--buildsystem=cmake -O--parallel dh_link -a -O--buildsystem=cmake -O--parallel dh_strip_nondeterminism -a -O--buildsystem=cmake -O--parallel dh_compress -a -O--buildsystem=cmake -O--parallel dh_compress: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_compress: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_compress: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_compress: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_fixperms -a -O--buildsystem=cmake -O--parallel dh_missing -a -O--buildsystem=cmake -O--parallel dh_missing: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_strip -a -O--buildsystem=cmake -O--parallel dh_strip: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_strip: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_strip: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_strip: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_makeshlibs -a -O--buildsystem=cmake -O--parallel dh_makeshlibs: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_shlibdeps -a -O--buildsystem=cmake -O--parallel dh_shlibdeps: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_shlibdeps: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_shlibdeps: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_shlibdeps: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_installdeb -a -O--buildsystem=cmake -O--parallel dh_installdeb: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_gencontrol -a -O--buildsystem=cmake -O--parallel dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package postgresql-13-rdkit: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit1: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-13-rdkit: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit1: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -a -O--buildsystem=cmake -O--parallel dh_builddeb -a -O--buildsystem=cmake -O--parallel dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202009.4-1_amd64.deb'. dpkg-deb: building package 'postgresql-13-rdkit-dbgsym' in '../postgresql-13-rdkit-dbgsym_202009.4-1_amd64.deb'. dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202009.4-1_amd64.deb'. dpkg-deb: building package 'librdkit1' in '../librdkit1_202009.4-1_amd64.deb'. dpkg-deb: building package 'postgresql-13-rdkit' in '../postgresql-13-rdkit_202009.4-1_amd64.deb'. dpkg-deb: building package 'librdkit1-dbgsym' in '../librdkit1-dbgsym_202009.4-1_amd64.deb'. dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202009.4-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../rdkit_202009.4-1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/rdkit-TKP8Bz /tmp/rdkit-202009.4-1y0w2m122 I: cleaning package lists and apt cache... W: deleting files in /tmp: tmp0jmbby4y W: deleting files in /tmp: texfonts I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.uspI2qVYGf... I: success in 17167.1813 seconds md5: librdkit-dev_202009.4-1_amd64.deb: OK md5: Value of 'md5' differs for librdkit1-dbgsym_202009.4-1_amd64.deb md5: Size differs for librdkit1-dbgsym_202009.4-1_amd64.deb md5: Value of 'md5' differs for librdkit1_202009.4-1_amd64.deb md5: Size differs for librdkit1_202009.4-1_amd64.deb md5: postgresql-13-rdkit-dbgsym_202009.4-1_amd64.deb: OK md5: postgresql-13-rdkit_202009.4-1_amd64.deb: OK md5: python3-rdkit-dbgsym_202009.4-1_amd64.deb: OK md5: python3-rdkit_202009.4-1_amd64.deb: OK sha1: librdkit-dev_202009.4-1_amd64.deb: OK sha1: Value of 'sha1' differs for librdkit1-dbgsym_202009.4-1_amd64.deb sha1: Size differs for librdkit1-dbgsym_202009.4-1_amd64.deb sha1: Value of 'sha1' differs for librdkit1_202009.4-1_amd64.deb sha1: Size differs for librdkit1_202009.4-1_amd64.deb sha1: postgresql-13-rdkit-dbgsym_202009.4-1_amd64.deb: OK sha1: postgresql-13-rdkit_202009.4-1_amd64.deb: OK sha1: python3-rdkit-dbgsym_202009.4-1_amd64.deb: OK sha1: python3-rdkit_202009.4-1_amd64.deb: OK sha256: librdkit-dev_202009.4-1_amd64.deb: OK sha256: Value of 'sha256' differs for librdkit1-dbgsym_202009.4-1_amd64.deb sha256: Size differs for librdkit1-dbgsym_202009.4-1_amd64.deb sha256: Value of 'sha256' differs for librdkit1_202009.4-1_amd64.deb sha256: Size differs for librdkit1_202009.4-1_amd64.deb sha256: postgresql-13-rdkit-dbgsym_202009.4-1_amd64.deb: OK sha256: postgresql-13-rdkit_202009.4-1_amd64.deb: OK sha256: python3-rdkit-dbgsym_202009.4-1_amd64.deb: OK sha256: python3-rdkit_202009.4-1_amd64.deb: OK Checksums: FAIL Cannot generate diffoscope for librdkit1-dbgsym_202009.4-1_amd64.deb: Cannot find URL: http://snapshot.notset.fr/mr/file/28f1227cca6ca2e1e28717d07f3f36b84e5c69c5e9f90829ae1142d5c163c5f9/download diffoscope run passed